Asus Thunderboltex II Card Not Working with Asus X99-Deluxe and Apple Thunderbolt Display

[biocentrism]

Hello

I am trying to install an Asus Thunderboltex II Card on my Asus X99-Deluxe motherboard but it is not working. The system fails to detect my Apple Thunderbolt Display.

I followed the instructions that came with the card. The instructions were written for pre-X99 boards and did not require the card to be inserted in any particular PCI-E slot. I tried several. The Asus website says that the X99-Deluxe is compatible with this card.

So I found some website where other people have had this problem. Some had success inserting this card into the "short" PCI-E slot (the second from the top). This did not work for me unfortunately.

I was wondering if anyone has been able to get this card to work on their X99, and if so, was there any particular trick in getting it to work.

Thank you.

 

[biocentrism]

Ok after 6 hours of troubleshooting and averting total disaster, I have finally figured out how to get my Asus Thunderboltex II Adapter Card working with my Asus X-99 Deluxe and Apple Thunderbolt Display.

Hopefully this will help others avoid the pain I have had to go through.

So here is what the problem was and what I did to resolve it:

0. Physically install the Thunderboltex card as per the instructions in the box. I tried various slots, from the bottom one, to a middle one, to the little one, and then finally the top one (I had to move my GPU which resulted in me ripping out a PCI-E slot and nearly destroying my motherboard but thankfully the computer still works. Read my other thread about this for the gory details).

1. Install the drivers from the CD in the box. I installed the drivers from the Asus website and they were from back in 2/14 before the release of X99. So I think the drivers in the box may be more up to date ironically.

2. I recently bought this computer from a high-end custom computer maker (which shall not be named). You would think that a company such as this would update the BIOS for you as standard procedure. Well they did not. The mobo was still using an old BIOS when a new one was released in 10/14 before my box was built. Turns out this BIOS is CRITICAL for this Thunderboltex to work on the X-99 Deluxe. (As an aside this is just one of several failing of this computer company and I am very disappointed with their product I must say. They sloppiness set off chain of events which has resulted in untold aggravation and nearly resulted in a very, very costly disaster).

3. So first step is to update your BIOS. To do this, I put in the disk that came with the mobo. I had to search around the menus to find a utility called Asus EZUpdater. Install this to your hard drive. Run it to update your BIOS. Restart.

4. In the now updated BIOS you go to Advanced > Intel Thunderbolt. Here are my settings:
a. all the toggles are ON, except TBT Device IO. These are the default settings anyways.
b. Security Level set to UniqueID (default)
c. TB Cache-line size set to 32 (default)
d. Basically everything set to default, except that you need to play around with AIC Location Group and AIC Location.

5. So what I figured out is this: when I put the Thunderboltex card in the very top slot (slot 1), then the settings that work are:
a. AIC Location Group: CPU0 NB PCIE Slot
b. AIC Location: NB PCIE X16_1

6. Now there are various websites out there which say you have to put the card in the "little" slot #2. But when I did this with the default settings of AIC Location Group: SB PCIE Slot, AIC Location: SB PCIE X4_1, it did not work. So after experimenting with them I got it to work.

7. So #4 is what works for me. If you want to put your GPU in slot #1, then you will have to play around with these 2 settings to get it to work for the slot you want to put it in.

8. After you boot up, you go to the bottom right corner and right click on Thunderbolt (you should see prompts saying that a new Thunderbolt device was detected and installing drivers). You get to the prompt to allow the Thunderbolt Display to connect and of course you choose Always.

That's it. Hope it helps. PM me if you get stuck and I will see if I can help.

Good luck.

 

[biocentrism]

Just an update, I have not been able to get 2 Apple TB Displays to work. Nor can I get 1 TB Diplays + 1 ACD Diplay to work. The 2nd screen remain blank.

Have read elsewhere of people having this issue but they are working on Hackintoshes. If anyone can get either 2TB or 1TB+1ACD to work on a PC Windows 7 please let me know.

 

[TrevorR]

I just bought the asus thunderbolt card just like yours and a z97-ar motherboard yesterday. I think all one would need to do is switch to onboard graphics. My monitor wouldn't light up but I could hear sound play from it so I knew it was connected. I didn't mess with the settings but all I did was switch the graphics from the GPU to the Onboard and it light up.

According to the instructions from ASUS, all you need to do is switch to onboard since you have to connect the asus card displayport to the motherboard display port.

It looks like you got it to work though by playing with the settings but all you need to do is switch to onboard and then you can use the lucidmvp software to utilize the gpu. This is exactly what the Asus instructions say as well.

 

[Blaketho]

I just bought the asus thunderbolt card just like yours and a z97-ar motherboard yesterday. I think all one would need to do is switch to onboard graphics. My monitor wouldn't light up but I could hear sound play from it so I knew it was connected. I didn't mess with the settings but all I did was switch the graphics from the GPU to the Onboard and it light up.

According to the instructions from ASUS, all you need to do is switch to onboard since you have to connect the asus card displayport to the motherboard display port.

It looks like you got it to work though by playing with the settings but all you need to do is switch to onboard and then you can use the lucidmvp software to utilize the gpu. This is exactly what the Asus instructions say as well.

Are you hooking to a thunderbolt display? I have an apple thunderbolt display and it would save me some money if I could hook a pc to it. I'm going with an asus Z97 pro mobo. I've never really used a pc outside of microsoft word so I wouldn't know how to set it all up.

 

[TrevorR]

I just bought the asus thunderbolt card just like yours and a z97-ar motherboard yesterday. I think all one would need to do is switch to onboard graphics. My monitor wouldn't light up but I could hear sound play from it so I knew it was connected. I didn't mess with the settings but all I did was switch the graphics from the GPU to the Onboard and it light up.

According to the instructions from ASUS, all you need to do is switch to onboard since you have to connect the asus card displayport to the motherboard display port.

It looks like you got it to work though by playing with the settings but all you need to do is switch to onboard and then you can use the lucidmvp software to utilize the gpu. This is exactly what the Asus instructions say as well.

Are you hooking to a thunderbolt display? I have an apple thunderbolt display and it would save me some money if I could hook a pc to it. I'm going with an asus Z97 pro mobo. I've never really used a pc outside of microsoft word so I wouldn't know how to set it all up.

I have an Apple 27" thunderbolt display. The asus Z97 Pro is listed as one of the cards that the Asus thunderboltex II card is compatible with. So all you would do is install the card per the instructions and fire up the pc on a regular monitor and then make sure the PC uses onboard graphics. Do not select automatic because it will utilize the GPU. This is my first PC build as well.

 

[Blaketho]

I just bought the asus thunderbolt card just like yours and a z97-ar motherboard yesterday. I think all one would need to do is switch to onboard graphics. My monitor wouldn't light up but I could hear sound play from it so I knew it was connected. I didn't mess with the settings but all I did was switch the graphics from the GPU to the Onboard and it light up.

According to the instructions from ASUS, all you need to do is switch to onboard since you have to connect the asus card displayport to the motherboard display port.

It looks like you got it to work though by playing with the settings but all you need to do is switch to onboard and then you can use the lucidmvp software to utilize the gpu. This is exactly what the Asus instructions say as well.

Are you hooking to a thunderbolt display? I have an apple thunderbolt display and it would save me some money if I could hook a pc to it. I'm going with an asus Z97 pro mobo. I've never really used a pc outside of microsoft word so I wouldn't know how to set it all up.

I have an Apple 27" thunderbolt display. The asus Z97 Pro is listed as one of the cards that the Asus thunderboltex II card is compatible with. So all you would do is install the card per the instructions and fire up the pc on a regular monitor and then make sure the PC uses onboard graphics. Do not select automatic because it will utilize the GPU. This is my first PC build as well.

How do you set it to onboard graphics or is that in the instructions as well?

 

[biocentrism]

I just bought the asus thunderbolt card just like yours and a z97-ar motherboard yesterday. I think all one would need to do is switch to onboard graphics. My monitor wouldn't light up but I could hear sound play from it so I knew it was connected. I didn't mess with the settings but all I did was switch the graphics from the GPU to the Onboard and it light up.

According to the instructions from ASUS, all you need to do is switch to onboard since you have to connect the asus card displayport to the motherboard display port.

It looks like you got it to work though by playing with the settings but all you need to do is switch to onboard and then you can use the lucidmvp software to utilize the gpu. This is exactly what the Asus instructions say as well.

The X99 is different from the Z97. The X99 does not have onboard video inputs like the Z97. I connected the DP cable from the Thunderboltex card to the GPU. The reason the 2nd TBD does not work I believe is that they need to be on separate video buses.

 

[Blaketho]

I just bought the asus thunderbolt card just like yours and a z97-ar motherboard yesterday. I think all one would need to do is switch to onboard graphics. My monitor wouldn't light up but I could hear sound play from it so I knew it was connected. I didn't mess with the settings but all I did was switch the graphics from the GPU to the Onboard and it light up.

According to the instructions from ASUS, all you need to do is switch to onboard since you have to connect the asus card displayport to the motherboard display port.

It looks like you got it to work though by playing with the settings but all you need to do is switch to onboard and then you can use the lucidmvp software to utilize the gpu. This is exactly what the Asus instructions say as well.

Are you hooking to a thunderbolt display? I have an apple thunderbolt display and it would save me some money if I could hook a pc to it. I'm going with an asus Z97 pro mobo. I've never really used a pc outside of microsoft word so I wouldn't know how to set it all up.

I have an Apple 27" thunderbolt display. The asus Z97 Pro is listed as one of the cards that the Asus thunderboltex II card is compatible with. So all you would do is install the card per the instructions and fire up the pc on a regular monitor and then make sure the PC uses onboard graphics. Do not select automatic because it will utilize the GPU. This is my first PC build as well.

I was also curious if you can use a thunderbolt monitor with another non thunderbolt display or two? (assuming the graphics card can support three monitors)

 

[biocentrism]

it depends on your set up. describe your set up?

generally, a TBD is built so that you can daisy chain other TBDs together. however, depending on your setup it may or may not work. you can also connect an ACD to a TBD as long as the ACD is at the end of the chain. but again, this may or may not work depending on your setup.

 

[Blaketho]

it depends on your set up. describe your set up?

generally, a TBD is built so that you can daisy chain other TBDs together. however, depending on your setup it may or may not work. you can also connect an ACD to a TBD as long as the ACD is at the end of the chain. but again, this may or may not work depending on your setup.

I have a MacBook Pro so I'm assuming I can easily hook that to a TBD and then another display using the second thunderbolt port with an adapter
With a pc I would want to hook it to the Thinderbolt display and a 27" non thunderbolt monitor.

 

[biocentrism]

it depends on your set up. describe your set up?

generally, a TBD is built so that you can daisy chain other TBDs together. however, depending on your setup it may or may not work. you can also connect an ACD to a TBD as long as the ACD is at the end of the chain. but again, this may or may not work depending on your setup.

I have a MacBook Pro so I'm assuming I can easily hook that to a TBD and then another display using the second thunderbolt port with an adapter
With a pc I would want to hook it to the Thinderbolt display and a 27" non thunderbolt monitor.

With a MBP you can hook up a TBD and non-TBD (assuming it has a mini-DP connector) using the plugs on the MBP.

On a PC you need to make sure you have a motherboard compatible with the Thunderboltex card and then, after following a lot of steps and possibly having to do a lot of troubleshooting, you can hook it up to a TBD. A non-TBD would have to be hooked up to the GPU or the motherboard. It probably won't work with the Thunderboltex. But from the sounds of it you are not that experienced in computers so I would get someone experienced to install it for you otherwise you are asking for huge frustration or worse.

 

[Blaketho]

it depends on your set up. describe your set up?

generally, a TBD is built so that you can daisy chain other TBDs together. however, depending on your setup it may or may not work. you can also connect an ACD to a TBD as long as the ACD is at the end of the chain. but again, this may or may not work depending on your setup.

I have a MacBook Pro so I'm assuming I can easily hook that to a TBD and then another display using the second thunderbolt port with an adapter
With a pc I would want to hook it to the Thinderbolt display and a 27" non thunderbolt monitor.

With a MBP you can hook up a TBD and non-TBD (assuming it has a mini-DP connector) using the plugs on the MBP.

On a PC you need to make sure you have a motherboard compatible with the Thunderboltex card and then, after following a lot of steps and possibly having to do a lot of troubleshooting, you can hook it up to a TBD. A non-TBD would have to be hooked up to the GPU or the motherboard. It probably won't work with the Thunderboltex. But from the sounds of it you are not that experienced in computers so I would get someone experienced to install it for you otherwise you are asking for huge frustration or worse.

Yeah planning my first build soon. I've ne'er built one but I am very technical. So assuming you can get the thunderbolt display working with the ex card you can just plug in the other monitor to the gpu? Sorry to ask so many questions im just trying to make a judgement call on a monitor for my build

 

[biocentrism]

if you are planning your first build i recommend doing a lot of research on each component to make sure they are compatible. before i bot the thunderboltex card i wanted to hook up 2 TBDs to it. i googled and it said that the thunderboltex ex would drive thunderbolt devices so i thot, "perfect, it will work". well little did i suspect that it would only drive 1 TBD and that you cannot drive a 2nd TBD or a 2nd ACD chained together. lesson here is "do your research". it is likely someone has tried it before and posted on a forum. make sure to google "not working" as well and "problem". as in, "asus thunderbolt card multiple displays not working". this way you find people who have tried it and had problems.

 

[Gilimanjaro]

Ok after 6 hours of troubleshooting and averting total disaster, I have finally figured out how to get my Asus Thunderboltex II Adapter Card working with my Asus X-99 Deluxe and Apple Thunderbolt Display.

Hopefully this will help others avoid the pain I have had to go through.

So here is what the problem was and what I did to resolve it:

0. Physically install the Thunderboltex card as per the instructions in the box. I tried various slots, from the bottom one, to a middle one, to the little one, and then finally the top one (I had to move my GPU which resulted in me ripping out a PCI-E slot and nearly destroying my motherboard but thankfully the computer still works. Read my other thread about this for the gory details).

1. Install the drivers from the CD in the box. I installed the drivers from the Asus website and they were from back in 2/14 before the release of X99. So I think the drivers in the box may be more up to date ironically.

2. I recently bought this computer from a high-end custom computer maker (which shall not be named). You would think that a company such as this would update the BIOS for you as standard procedure. Well they did not. The mobo was still using an old BIOS when a new one was released in 10/14 before my box was built. Turns out this BIOS is CRITICAL for this Thunderboltex to work on the X-99 Deluxe. (As an aside this is just one of several failing of this computer company and I am very disappointed with their product I must say. They sloppiness set off chain of events which has resulted in untold aggravation and nearly resulted in a very, very costly disaster).

3. So first step is to update your BIOS. To do this, I put in the disk that came with the mobo. I had to search around the menus to find a utility called Asus EZUpdater. Install this to your hard drive. Run it to update your BIOS. Restart.

4. In the now updated BIOS you go to Advanced > Intel Thunderbolt. Here are my settings:
a. all the toggles are ON, except TBT Device IO. These are the default settings anyways.
b. Security Level set to UniqueID (default)
c. TB Cache-line size set to 32 (default)
d. Basically everything set to default, except that you need to play around with AIC Location Group and AIC Location.

5. So what I figured out is this: when I put the Thunderboltex card in the very top slot (slot 1), then the settings that work are:
a. AIC Location Group: CPU0 NB PCIE Slot
b. AIC Location: NB PCIE X16_1

6. Now there are various websites out there which say you have to put the card in the "little" slot #2. But when I did this with the default settings of AIC Location Group: SB PCIE Slot, AIC Location: SB PCIE X4_1, it did not work. So after experimenting with them I got it to work.

7. So #4 is what works for me. If you want to put your GPU in slot #1, then you will have to play around with these 2 settings to get it to work for the slot you want to put it in.

8. After you boot up, you go to the bottom right corner and right click on Thunderbolt (you should see prompts saying that a new Thunderbolt device was detected and installing drivers). You get to the prompt to allow the Thunderbolt Display to connect and of course you choose Always.

That's it. Hope it helps. PM me if you get stuck and I will see if I can help.

Good luck.

So I've half gotten my Z97 Gryphon build to work also with the ThunderboltEX/II.

I have my discrete GPU on PCIEX16_3 looped through the ThunderboltEX/II on PCIEX16_1 (though the manual 'recommends' PCIEX16_3 for the Thunderbolt card).

Video and audio works on my Thunderbolt-display. I suspect audio is just part of the displayport throughput, which I think works as long as the ThunderboltEX gets power. But the Thunderbolt software is not seeing any devices, so I suspect the 'other part' is not working yet, and that's probably related to the PCI slot.

Problem is, swapping slots with the GPU won't work as I can't fit the GPU which has a backplate in slot 1 due to the size of my CPU heatsink.

I guess I'll try with onboard video and the TB in the 3rd slot, but I would really love some more comprehensive info on the BIOS settings (though I guess they're different between the X99 and Z97; my AOC location selections are just plain numbers from 0 to 8 IIRC).

Any clue where to find more info?

Thanks, G

 

[alfredomova]

Same problem here... I have an Asus X-99 Deluxe/u3.1, two GTX 970 Strix and the thunderbolt ex/II... y have the cards in this order:

PCIEX16_1 -- FIRST GTX 970
PCIEX4_1 -- Nothing and disabled in the bios/uefi (hidden under the gtx)
PCIEX16_2 -- ThunderboltEX
PCIEX16_3 -- SECOND GTX 970
PCIEX16_4 -- nothing (hidden under the gtx)
PCIEX16_5 -- nothing

have Video and Audio but no USB, firewire, ethernet, isight from the Apple Thunderbolt display...

with a single GTX and the ThunderboltEX in the PCIEX16_5 changing:

AIC Location Group >>> CPU0 NB PCIE Slot
AIC Location >>> NB PCIE X16_5

i was able to use the camera, usb etc.. but when i installed (and since then) the second GTX the system wouldn't even POST... 🙁 i had to clear_cmos and restore default config

https://youtu.be/IXClf5U2-Sc

take a look at my problem so far:

http://linustechtips.com/main/topic/404336-x-99-deluxeu31-2way-sli-gtx-970-strix-not-working/

http://www.hardwarecanucks.com/forum/troubleshooting/69817-x-99-deluxe-u3-1-2way-sli-gtx-970-strix-thunderboltex-ii-not-working.html

http://www.tomshardware.com/answers/id-2715468/deluxe-2way-sli-gtx-970-strix-working.html

🙁

 

[TrevorR]

Same problem here... I have an Asus X-99 Deluxe/u3.1, two GTX 970 Strix and the thunderbolt ex/II... y have the cards in this order:

PCIEX16_1 -- FIRST GTX 970
PCIEX4_1 -- Nothing and disabled in the bios/uefi (hidden under the gtx)
PCIEX16_2 -- ThunderboltEX
PCIEX16_3 -- SECOND GTX 970
PCIEX16_4 -- nothing (hidden under the gtx)
PCIEX16_5 -- nothing

have Video and Audio but no USB, firewire, ethernet, isight from the Apple Thunderbolt display...

with a single GTX and the ThunderboltEX in the PCIEX16_5 changing:

AIC Location Group >>> CPU0 NB PCIE Slot
AIC Location >>> NB PCIE X16_5

i was able to use the camera, usb etc.. but when i installed (and since then) the second GTX the system wouldn't even POST... 🙁 i had to clear_cmos and restore default config

https://youtu.be/IXClf5U2-Sc

take a look at my problem so far:

http://linustechtips.com/main/topic/404336-x-99-deluxeu31-2way-sli-gtx-970-strix-not-working/

http://www.hardwarecanucks.com/forum/troubleshooting/69817-x-99-deluxe-u3-1-2way-sli-gtx-970-strix-thunderboltex-ii-not-working.html

http://www.tomshardware.com/answers/id-2715468/deluxe-2way-sli-gtx-970-strix-working.html

🙁

How did you get the camera and usb ports to work? Apple doesn't make the drivers for windows?

I had an issue that was just like yours, constant reboot loop. Turns out one of the wires came off the connector and I had to resolder it on and it booted. Maybe check that.

Also, the TB card only works in lowest PCI port, in your case 5. It doesn't work anywhere else if you want to use SLI.

 

[alfredomova]

Same problem here... I have an Asus X-99 Deluxe/u3.1, two GTX 970 Strix and the thunderbolt ex/II... y have the cards in this order:

PCIEX16_1 -- FIRST GTX 970
PCIEX4_1 -- Nothing and disabled in the bios/uefi (hidden under the gtx)
PCIEX16_2 -- ThunderboltEX
PCIEX16_3 -- SECOND GTX 970
PCIEX16_4 -- nothing (hidden under the gtx)
PCIEX16_5 -- nothing

have Video and Audio but no USB, firewire, ethernet, isight from the Apple Thunderbolt display...

with a single GTX and the ThunderboltEX in the PCIEX16_5 changing:

AIC Location Group >>> CPU0 NB PCIE Slot
AIC Location >>> NB PCIE X16_5

i was able to use the camera, usb etc.. but when i installed (and since then) the second GTX the system wouldn't even POST... 🙁 i had to clear_cmos and restore default config

https://youtu.be/IXClf5U2-Sc

take a look at my problem so far:

http://linustechtips.com/main/topic/404336-x-99-deluxeu31-2way-sli-gtx-970-strix-not-working/

http://www.hardwarecanucks.com/forum/troubleshooting/69817-x-99-deluxe-u3-1-2way-sli-gtx-970-strix-thunderboltex-ii-not-working.html

http://www.tomshardware.com/answers/id-2715468/deluxe-2way-sli-gtx-970-strix-working.html

🙁

How did you get the camera and usb ports to work? Apple doesn't make the drivers for windows?

I had an issue that was just like yours, constant reboot loop. Turns out one of the wires came off the connector and I had to resolder it on and it booted. Maybe check that.

Also, the TB card only works in lowest PCI port, in your case 5. It doesn't work anywhere else if you want to use SLI.

Hi! pretty easy actually 😀 i installed boot camp 😀
follow this guide:
http://duntuk.com/how-install-apple-thunderbolt-display-non-apple-thunderbolt-pc-brightness-control-support

and that's actually how I tested that the thunderbolt card was working right (with only 1 gtx...) b'cos i could use the iShight camera

have you try SLI + thunderbolt in your pc? 'cos I have try every port y cant get out of the reboot loop 🙁 i'm really stuck with that, and for the wire, as far as the last time i open the case it was fine... i think... i'l have to double check..

thanks for your answer!

 

[FredericoMF]

Hello

I am trying to install an Asus Thunderboltex II Card on my Asus X99-Deluxe motherboard but it is not working. The system fails to detect my Apple Thunderbolt Display.

I followed the instructions that came with the card. The instructions were written for pre-X99 boards and did not require the card to be inserted in any particular PCI-E slot. I tried several. The Asus website says that the X99-Deluxe is compatible with this card.

So I found some website where other people have had this problem. Some had success inserting this card into the "short" PCI-E slot (the second from the top). This did not work for me unfortunately.

I was wondering if anyone has been able to get this card to work on their X99, and if so, was there any particular trick in getting it to work.

Thank you.

Hi biocentrism ,
Great job! Looks like you had a lot of work.
I also have an X99-Deluxe and an Apple Thunderbolt Display, and was wondering if all this stuff is gonna work for an Asus ThunderboltEXII -DUAL. Looks like they don't sell the single model anymore.
You didn't mention, but from your post I guess that your ThunderboltEXII card is the single one. Also, there is another issue, some devices/models have a data transfer rate up to 10GB/s and others up to 20 GB/s. So, I'm not sure which one to buy. Will the X99-Deluxe support 20GB/s transfer rate?. Could you tell me the data transfer rate of your thunderbolt card?
I really appreciate your help.
Best.

 

[FredericoMF]

4. In the now updated BIOS you go to Advanced > Intel Thunderbolt. Here are my settings:
a. all the toggles are ON, except TBT Device IO. These are the default settings anyways.
b. Security Level set to UniqueID (default)
c. TB Cache-line size set to 32 (default)
d. Basically everything set to default, except that you need to play around with AIC Location Group and AIC Location.

Hi biocentrism,
I have the same mobo X-99DELUXE and have been unsuccessfully trying to connect my TB monitor using a Thunderbolt EXII extension card. After BIOS update (version 1801 - the latest) I couldn't be able to find the "Intel Thunderbolt" and the following options mentioned above. Could you tell me your BIOS version, perhaps I can downgrade.
Best.

 

[irenabyss]

Hi biocentrism,
I have the same mobo X-99DELUXE and have been unsuccessfully trying to connect my TB monitor using a Thunderbolt EXII extension card. After BIOS update (version 1801 - the latest) I couldn't be able to find the "Intel Thunderbolt" and the following options mentioned above. Could you tell me your BIOS version, perhaps I can downgrade.
Best.

Success with the following configuration with Thunderbolt display routing and thunderbolt drive access in both Windows 10 and hackintosh OS X 10.10 (not no hot swapping in OS X)
ASUS X99-DELUXE BIOS Version 1901
Intel Core i7 5930K
Intel NVME 750 Series 1.2TB PCI card as windows boot drive
EVGA GeForce GTX 970 4GB
ThunderboltEX II Card
Clover Bootloader
Windows 10 / Hackintosh OSX 10.10 Yosemite
I found Josh Olsons description at the link below to be most useful and have added my install steps on stack exchange at:
http://superuser.com/questions/869494/thunderbolt-on-pc-on-an-x99-motherboard-and-the-r9-295x2?answertab=oldest#tab-top
Thanks to everyone who contributed system info here with this and other forums I finally got success.

 

[FredericoMF]

Success with the following configuration with Thunderbolt display routing and thunderbolt drive access in both Windows 10 and hackintosh OS X 10.10 (not no hot swapping in OS X)
ASUS X99-DELUXE BIOS Version 1901
Intel Core i7 5930K
Intel NVME 750 Series 1.2TB PCI card as windows boot drive
EVGA GeForce GTX 970 4GB
ThunderboltEX II Card
Clover Bootloader
Windows 10 / Hackintosh OSX 10.10 Yosemite
I found Josh Olsons description at the link below to be most useful and have added my install steps on stack exchange at:
http://superuser.com/questions/869494/thunderbolt-on-pc-on-an-x99-motherboard-and-the-r9-295x2?answertab=oldest#tab-top
Thanks to everyone who contributed system info here with this and other forums I finally got success.

Hi irenabyss,
Thanks for answer and the nice report as well. Except for the NVME card, I have almost the same hardware. I have been using the BIOS upgrade file (ASUS X99-DELUXE BIOS Version 1901) from ASUS homepage , however, I couldn't found the BIOS option "Intel Thunderbolt" under the "Advanced" menu. It's not clear to me, but do I have to see it independent of the TB-EXII card detection itself? or it's going to appear there just after the BIOS upgrade? In other words, do I have to change the slot position of the GPU and the TB card until the "Intel Thunderbolt" option appears? I'm puzzled, don't know if the card has been detected or not and if the BIOS upgrade didn't work.
Best.