TL;DR
* ThunderboltEX card can interfer with GPUs in CSM mode (disable CSM if possible). My R9 295x2 needed to have UEFI enabled by installing a vbios update (not a windows driver update).
* ThunderboltEX card can go in just about any slot, but it should probably go on the southbridge PCIe (the instructions that come with the card are useless here).
* Rampage V Extreme needed a bios update to 0901 because using the southbridge PCIe slot meant you should disable SATAExpress (the ASM106SE chip).
* Most of the Thunderbolt bios settings don't do anything useful (for the typical end user) except setting the cache-line size as high as it'll go or if you have really old thunderbolt devices changing the security level to "Legacy".
Some background. I was a MS user for many years from Dos 6.22 though Windows XP then I switched to mac about a decade ago and now use a Macbook Pro with Thunderbolt monitor. This past fall I wanted to get back into PC gaming and decided to build "The Beast" an Asus Rampage V Extreme, 32 GB DDR4 RAM, i7-5930k with liquid cooling, VisionTek R9 295x2 8GB (the reference design not their OC design), a Samsung XP941 512 GB SSD, and to top it off a ThunderboltEX II Dual so I can use my Sweet Thunderbolt Monitor. Now I've built several computers for myself in the past and helped with building, debugging, maintaning, etc. for dozens more computer, but until this build I have never been so completely stumped and frustrated with hardware in my life.
There is almost ZERO (user level) documentation on Thunderbolt for PC (I hope to remedy some of this with this post). My problem began a few weeks after my basic build (early November 2014) when I got my ThunderboltEX card (also a pain in the ass, you can't find them in stock anywhere). So, I install the card and all of a sudden my bios start boot looping during hardware initialization (Q code 79, CSM initialization). This indicates it's an issue with hardware that doesn't have UEFI bios and CSM is the Compatiblity Support Module. After updating the BIOS to 0802 there were no changes. The other problem is that I had no idea what a working Thunderbolt card with no devices looked like on windows, since the OS drivers installed no problem and didn't complain about anything. This [http://imagescdn.tweaktown.com/content/6/2/6249_30_thunderbolt_2_ready_for_windows_with_the_asus_thunderboltex_ii.png] is what it's supposed to look like, mine was just empty no root thunderbolt port(s).
I quickly track it down (wrongly) to the ThunderboltEX card, if it's in it doesn't work, other it's fine. So, I begin researching this. The instructions are aimed at the Z87 chipset (my inital fear is that the X99 boards weren't supported, all of them are as long as they have the TB_HEADER pins) and always describe putting the card into the last PCIe slot (only other setting that seemed to make much difference was the cache-line size [http://www.tweaktown.com/articles/6249/thunderbolt-2-ready-for-windows-with-the-asus-thunderboltex-ii/index3.html] . This is wrong on the Rampage V Extreme, it can be place in almost an PCIe slot as long as you configure it properly, but the default slot is the southbridge (SB) controller slot (goodluck getting specifics on which PCIe lanes are northbridge (NB) or southbridge(SB) Hint: northbridge is your graphics cards usually and many mobos color code them, that narrows it down, but on my board that still left three mystery PCIe slots, only one of which was SB) which is the full length black slot on the Rampage.
This didn't help and after a stop at Fry's to get an X99 Deluxe to test the card with and still not being able to get it to work, ASUS (I was pretty impressed, it seems they have hardware benches there for the tech support to support you with) and I decide it must be an issue with the ThunderboltEX card (we were probablly wrong), so I return the ThunderboltEX card for a refund and order a new one from another Amazon vendor (because the vendor I bought from initially only had the single one in stock, which seems to be common as of December 2014).
In the mean time I happend to aquire some older ATI cards a 5xxx and a 7xxx. Plopping the new card in had the same problems (now early December). So fuck it I give up for now everything is great except I can't use my Thunderbolt monitor on it, plug in a 32" TV and we're good for now.
Fast forward to today (January 25 2015). I try again and end up in the same boot loop. I check for a bios update and they've released 0901 [http://rog.asus.com/forum/showthread.php?54383-Bios-0901], which causes cards in PCIe_x4_1 to not be detected if the ASM106SE (SATAEXPRESS) chip is disabled. "Holy shit!," I thought. That's the slot the thunderbolt card goes is (by default) and I disable sata express because I can't use it anyway with that card in there. Nope, not the problem (although it could have been a problem once I worked out the main issue). This time I also tried disabling my CSM to try and work around the Q code 79. Nope, video card "drivers" don't support UEFI. "The VGA card is not supported by UEFI driver"
Finally I contact ASUS again and my rep doesn't know, but there's a guy there that's pretty versed in either the bios or the Thunderbolt card because before they hang up (without a resolution) they says it's probably your bios on your video card; update that. "WTF update my videocard bios?!?," I think, "I've never even heard of needing to do that. Drivers sure, but not the bios." Well, that left me stumped for a bit and start doing forum searches on that and find a couple of references to UEFI GPU bios'. Finally, I connect the dots and swap my 295x2 with my 7xxx and BAM! Thunderbolt works like a charm!
I disable the Thunderbolt card pop my 295x2 back in and start search more. Turns out that many modern graphics cards (since late 2012 [http://forums.pugetsystems.com/threads/5919-Secure-Boot-UEFI-Windows-8-Oh-My!]) have the UEFI drivers (really bios, I guess) built in (and enabled), but not the 295x2. Something about having two chips on the same card, but the bios is there just not enabled this [http://www.overclock.net/t/1483021/official-amd-r9-295x2-owners-club/1530#post_22631742] (this is a generic ATI bios, so should work with most reference cards) post had the same version of the drivers as my card, but has UEFI enabled. I just installed them with ATIWinFlash [http://www.overclock.net/t/1353325/tutorial-atiwinflash-how-to-flash-the-bios-of-your-ati-cards] rebooted, disabled CSM again. This time it boots without and error, I enable Thunderbolt again. This time everything is working perfectly and I'm playing Dragon Age on my awsome Thunderbolt Display.
* ThunderboltEX card can interfer with GPUs in CSM mode (disable CSM if possible). My R9 295x2 needed to have UEFI enabled by installing a vbios update (not a windows driver update).
* ThunderboltEX card can go in just about any slot, but it should probably go on the southbridge PCIe (the instructions that come with the card are useless here).
* Rampage V Extreme needed a bios update to 0901 because using the southbridge PCIe slot meant you should disable SATAExpress (the ASM106SE chip).
* Most of the Thunderbolt bios settings don't do anything useful (for the typical end user) except setting the cache-line size as high as it'll go or if you have really old thunderbolt devices changing the security level to "Legacy".
Some background. I was a MS user for many years from Dos 6.22 though Windows XP then I switched to mac about a decade ago and now use a Macbook Pro with Thunderbolt monitor. This past fall I wanted to get back into PC gaming and decided to build "The Beast" an Asus Rampage V Extreme, 32 GB DDR4 RAM, i7-5930k with liquid cooling, VisionTek R9 295x2 8GB (the reference design not their OC design), a Samsung XP941 512 GB SSD, and to top it off a ThunderboltEX II Dual so I can use my Sweet Thunderbolt Monitor. Now I've built several computers for myself in the past and helped with building, debugging, maintaning, etc. for dozens more computer, but until this build I have never been so completely stumped and frustrated with hardware in my life.
There is almost ZERO (user level) documentation on Thunderbolt for PC (I hope to remedy some of this with this post). My problem began a few weeks after my basic build (early November 2014) when I got my ThunderboltEX card (also a pain in the ass, you can't find them in stock anywhere). So, I install the card and all of a sudden my bios start boot looping during hardware initialization (Q code 79, CSM initialization). This indicates it's an issue with hardware that doesn't have UEFI bios and CSM is the Compatiblity Support Module. After updating the BIOS to 0802 there were no changes. The other problem is that I had no idea what a working Thunderbolt card with no devices looked like on windows, since the OS drivers installed no problem and didn't complain about anything. This [http://imagescdn.tweaktown.com/content/6/2/6249_30_thunderbolt_2_ready_for_windows_with_the_asus_thunderboltex_ii.png] is what it's supposed to look like, mine was just empty no root thunderbolt port(s).
I quickly track it down (wrongly) to the ThunderboltEX card, if it's in it doesn't work, other it's fine. So, I begin researching this. The instructions are aimed at the Z87 chipset (my inital fear is that the X99 boards weren't supported, all of them are as long as they have the TB_HEADER pins) and always describe putting the card into the last PCIe slot (only other setting that seemed to make much difference was the cache-line size [http://www.tweaktown.com/articles/6249/thunderbolt-2-ready-for-windows-with-the-asus-thunderboltex-ii/index3.html] . This is wrong on the Rampage V Extreme, it can be place in almost an PCIe slot as long as you configure it properly, but the default slot is the southbridge (SB) controller slot (goodluck getting specifics on which PCIe lanes are northbridge (NB) or southbridge(SB) Hint: northbridge is your graphics cards usually and many mobos color code them, that narrows it down, but on my board that still left three mystery PCIe slots, only one of which was SB) which is the full length black slot on the Rampage.
This didn't help and after a stop at Fry's to get an X99 Deluxe to test the card with and still not being able to get it to work, ASUS (I was pretty impressed, it seems they have hardware benches there for the tech support to support you with) and I decide it must be an issue with the ThunderboltEX card (we were probablly wrong), so I return the ThunderboltEX card for a refund and order a new one from another Amazon vendor (because the vendor I bought from initially only had the single one in stock, which seems to be common as of December 2014).
In the mean time I happend to aquire some older ATI cards a 5xxx and a 7xxx. Plopping the new card in had the same problems (now early December). So fuck it I give up for now everything is great except I can't use my Thunderbolt monitor on it, plug in a 32" TV and we're good for now.
Fast forward to today (January 25 2015). I try again and end up in the same boot loop. I check for a bios update and they've released 0901 [http://rog.asus.com/forum/showthread.php?54383-Bios-0901], which causes cards in PCIe_x4_1 to not be detected if the ASM106SE (SATAEXPRESS) chip is disabled. "Holy shit!," I thought. That's the slot the thunderbolt card goes is (by default) and I disable sata express because I can't use it anyway with that card in there. Nope, not the problem (although it could have been a problem once I worked out the main issue). This time I also tried disabling my CSM to try and work around the Q code 79. Nope, video card "drivers" don't support UEFI. "The VGA card is not supported by UEFI driver"
Finally I contact ASUS again and my rep doesn't know, but there's a guy there that's pretty versed in either the bios or the Thunderbolt card because before they hang up (without a resolution) they says it's probably your bios on your video card; update that. "WTF update my videocard bios?!?," I think, "I've never even heard of needing to do that. Drivers sure, but not the bios." Well, that left me stumped for a bit and start doing forum searches on that and find a couple of references to UEFI GPU bios'. Finally, I connect the dots and swap my 295x2 with my 7xxx and BAM! Thunderbolt works like a charm!
I disable the Thunderbolt card pop my 295x2 back in and start search more. Turns out that many modern graphics cards (since late 2012 [http://forums.pugetsystems.com/threads/5919-Secure-Boot-UEFI-Windows-8-Oh-My!]) have the UEFI drivers (really bios, I guess) built in (and enabled), but not the 295x2. Something about having two chips on the same card, but the bios is there just not enabled this [http://www.overclock.net/t/1483021/official-amd-r9-295x2-owners-club/1530#post_22631742] (this is a generic ATI bios, so should work with most reference cards) post had the same version of the drivers as my card, but has UEFI enabled. I just installed them with ATIWinFlash [http://www.overclock.net/t/1353325/tutorial-atiwinflash-how-to-flash-the-bios-of-your-ati-cards] rebooted, disabled CSM again. This time it boots without and error, I enable Thunderbolt again. This time everything is working perfectly and I'm playing Dragon Age on my awsome Thunderbolt Display.
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