Originally Posted by itsakjt
Try updating to the latest drivers. Remove any unwanted software and check the system. It is very unlikely that the PCIE slot is faulty. But it may happen. Also check the BIOS and disable any overclocking. Run everything at factory settings and check results.
i have actually had a fault pcie slot, and it would only run at 8x... and ultimately it did not allow any cards to work it i it... (sabertooth 990fx) i RMA'd and all is well.
nothing much you can do to diagnose it except to compare performance across same pcie slots.
and try different graphics cards and look in gpu-z to see the width of the pcie slot that is defective and what it should be.
Btw supposedly a pcie3 8x slot is the same as a pcie2 16x slot.