Hello, I purchased an MSI GTX 980 gaming 4G graphics card yesterday and encountered the very problem straight away while connecting it to Intel DZ87KLT-75K motherboard.
The problem is motherboards PCI-e x16 v3 port doesnt connect the graphics card to its full transfer rate. Instead of transferring 8GT/s it now connect gtx 980 as PCI-e x16 v1.1 @ transfer rate of 2.5GT/s
I have two of these boards, immediately replaced the motherboard with exact another copy nothing changes. BIOS shows PCI-E x16 2.5GT/s and GPU-Z reports the graphics card is capable to connect through PCI-e x16 v3 but currently connected from PCI-e x16 v1.1.
I searched the forum. Found not much response as very few people purchased this board. I have used almost every BIOS versions to check whether it was causing the issue or not and surprisingly any of those available BIOS versions doesn't fix it.
I tried other PCI express ports with no luck and totally stuck here. Using the card at reduced transfer speed. I actually haven't had this issue with sapphire radeon vapor0x 7970 ghz edition.