Question Graphics card only works in MB x4 PCIe slot

Oct 19, 2021
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I apologize in advance for the long post. First of all here are the specs of my build:
  • MB: Gigabyte B450 Aorus Elite;
  • CPU: AMD Ryzen 5 3600;
  • GPU: MSI GeForce RTX 2060 Super Ventus GP OC, 8GB;
  • RAM: G.Skill Ripjaws V DDR4 3200mhz CL16 (2x8GB);
  • SSD: Intel 660P, 1TB, M.2 NVME;
  • PSU: Corsair 550W 80 Plus Bronze CX550.
This setup worked fined for many months with the graphics card installed in the x16 top PCIe slot, until a few months back, when I was installing a new CPU cooler and had to remove the GPU to make it easier to fit. When I installed the GPU back in the x16 slot, I forgot to plug in the GPU PSU cable before powering on the system. I quickly realised this, shut everything down, connected the cable and tried again, but was unnable to get a post. The VGA LED on the MB was also on when powering on, indicating a problem with the graphics card.

After some panicked googling I tried reseting the CMOS, reinstalling the RAM and a bunch of other things that did nothing. After a while I placed the GPU in the bottom x4 slot and the system powered on and posted normally. Installing it again on the x16 slot still did not work. This, along with some forum posts saying that turning the system on without the PSU cable connected to the GPU could mess up the internal circuits of the board, made me think the problem was with the MB. To confirm the GPU was fine, I tested it with a friend's system and it worked fine in the x16 slot. I then sent the MB to Gigabyte to fix the problem, but according to them the board was working fine. They ran some standard tests and sent it back to me. I then sent it to them again claiming the issue was still present and they said once again that the board was fine, and even sent me a video of a graphics card installed in the x16 slot and the system powering on and posting.

I have also tried updating the BIOS (including the GPU's) and even reinstalling Windows, with no success. The only thing I haven't tried is installing a different graphics card in the x16 slot myself, since I don't have access to one, but the video from Gigabyte proves it works with a different GPU. I have been using the pc with the GPU in the x4 slot, but the performance in some games is not the same... I don't know what else I can try to do to figure out what is wrong and any help or insight is much appreciated.
 
I apologize in advance for the long post. First of all here are the specs of my build:
  • MB: Gigabyte B450 Aorus Elite;
  • CPU: AMD Ryzen 5 3600;
  • GPU: MSI GeForce RTX 2060 Super Ventus GP OC, 8GB;
  • RAM: G.Skill Ripjaws V DDR4 3200mhz CL16 (2x8GB);
  • SSD: Intel 660P, 1TB, M.2 NVME;
  • PSU: Corsair 550W 80 Plus Bronze CX550.
This setup worked fined for many months with the graphics card installed in the x16 top PCIe slot, until a few months back, when I was installing a new CPU cooler and had to remove the GPU to make it easier to fit. When I installed the GPU back in the x16 slot, I forgot to plug in the GPU PSU cable before powering on the system. I quickly realised this, shut everything down, connected the cable and tried again, but was unnable to get a post. The VGA LED on the MB was also on when powering on, indicating a problem with the graphics card.

After some panicked googling I tried reseting the CMOS, reinstalling the RAM and a bunch of other things that did nothing. After a while I placed the GPU in the bottom x4 slot and the system powered on and posted normally. Installing it again on the x16 slot still did not work. This, along with some forum posts saying that turning the system on without the PSU cable connected to the GPU could mess up the internal circuits of the board, made me think the problem was with the MB. To confirm the GPU was fine, I tested it with a friend's system and it worked fine in the x16 slot. I then sent the MB to Gigabyte to fix the problem, but according to them the board was working fine. They ran some standard tests and sent it back to me. I then sent it to them again claiming the issue was still present and they said once again that the board was fine, and even sent me a video of a graphics card installed in the x16 slot and the system powering on and posting.

I have also tried updating the BIOS (including the GPU's) and even reinstalling Windows, with no success. The only thing I haven't tried is installing a different graphics card in the x16 slot myself, since I don't have access to one, but the video from Gigabyte proves it works with a different GPU. I have been using the pc with the GPU in the x4 slot, but the performance in some games is not the same... I don't know what else I can try to do to figure out what is wrong and any help or insight is much appreciated.
The GPU slot's 16 PCIe lane are fed by the CPU so while it's rare the problem could be in the CPU, not motherboard. If you have access to one try testing with another AM4 CPU in your motherboard mainly just to see if the GPU works in the correct slot. Be sure to reset CMOS each time you swap CPU's.
 
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Reactions: Historical Fidelity
May 21, 2021
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Check your graphics cards contacts pads on its pci-e connector. Are any of them rusted out or discolored/have material buildup on them? At this point (with the MB manufacturer giving you a video of a graphics card working on your MB and the graphics card working on your friends pc) I think it might be bad conductor contact between your graphics card and MB pci-e slot. Even a couple micrometers difference in how the conductors in the slot and the GC’s connector contact can mean the difference between good and faulty signal (which might be why your GC works in your friends pc). Hope this helps
 
Oct 19, 2021
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You should have sent them you gpu with the motherboard so they could trouble shoot it . What gpu did they use to test the slot?
Since it was under warranty they said I could only send the MB back. They tested it with an RTX 2080 Super and sent a video of the system powering on, even showing the S/N proving it was my board.
 
Oct 19, 2021
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The GPU slot's 16 PCIe lane are fed by the CPU so while it's rare the problem could be in the CPU, not motherboard. If you have access to one try testing with another AM4 CPU in your motherboard mainly just to see if the GPU works in the correct slot. Be sure to reset CMOS each time you swap CPU's.
Oh I had not considered that it could be the CPU... I hope it isn't cause my warranty has already expired and they are crazy expensive nowadays where I live. I'm going to try and get a hold of another one to test with my MB and will post an update here. Thanks a lot for the tip!
 
Oct 19, 2021
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Check your graphics cards contacts pads on its pci-e connector. Are any of them rusted out or discolored/have material buildup on them? At this point (with the MB manufacturer giving you a video of a graphics card working on your MB and the graphics card working on your friends pc) I think it might be bad conductor contact between your graphics card and MB pci-e slot. Even a couple micrometers difference in how the conductors in the slot and the GC’s connector contact can mean the difference between good and faulty signal (which might be why your GC works in your friends pc). Hope this helps
I checked all the contacts and they looked fine to me... I also cleaned them with isopropyl alcohol and tried again with no luck... But thank you for your input!
 
Oct 19, 2021
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While installing new cpu cooler, did you accidentally drop your cpu?
Perhaps some cpu pins got bent or broken off?
Nope, I didn't even remove the CPU when installing the new cooler, just removed the old one and cleaned the thermal paste. I did remove it for sending the MB to the manufacturer, but it was after the problem had already occurred plus I was really careful when removing and storing it in its original package.
 
Oct 19, 2021
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If we go all the way back to the beginning, and list what we have, Gpu worked fine until you installed a cooler. What kind of cooler did you install?
I removed the stock cooler to install a Cooler Master AIO water cooler.

Oh and I have read up on the consequences of starting a pc up without the gpu powered up and there are none.
I read somewhere that in doing this, the GPU would try to draw power from the PCIe slot itself, which could damage the internal tracks of the MB... But now that I know that the CPU is what powers the x16 slot I'm thinking maybe something is wrong with it, not the MB.
 
I removed the stock cooler to install a Cooler Master AIO water cooler.


I read somewhere that in doing this, the GPU would try to draw power from the PCIe slot itself, which could damage the internal tracks of the MB... But now that I know that the CPU is what powers the x16 slot I'm thinking maybe something is wrong with it, not the MB.
So I would first try and loosen the cooling plate somwwhat on the cpu. I had a situation where I had tightened the cooling plate down to much, and it wasn't a reckless amount, maybe two turns of the screws to loosen the cooling plate and the pc posted. Perhaps try this. If this doesn't work I would inspect your pins to make sure the cooling plate was not tightened down too much on the cpu and slightly bent one or two pins.
 
Oct 19, 2021
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Update: this weekend I traveled to visit a friend who's got a similar pc and we tested a bunch of different hw combinations... I ruled out the CPU as being the problem because I tested it in his MB with my graphics card in the x16 slot and it worked fine. I also inspected and cleaned the pins with isopropyl and tried less clamping force with the cooler pump with no luck.

We also tried his Ryzen 5 2600 on my MB and didn't get a post, but this time instead of the VGA, the DRAM LED was lit up, even with his RAM sticks installed (weird). At this point I'm fairly confident that the MB is the issue, even though I still can't explain the video Gigabyte sent me.. It doesn't matter anyway cause my warranty has now expired. I think I'll wait for black friday deals to buy a new one and see if that finally solves it.

Thanks a lot to everyone that responded!!
 

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