MSI GTX 980 running at PCI-E X2 3.0?

[Psylantwolf]

Hello, all! This is my first post here, and sadly, it isn't a happy story.

My MSI GTX 980,
this one: http://www.newegg.com/Product/Product.aspx?Item=N82E16814127834
-is only running at PCI-E X2 3.0 (and some times flickers down to 1.1).

I thought this may just be an error with GPUZ's reporting, so I did some benchmarks. Sure enough, when a benchmark is not bandwidth heavy, like FurMark, it performs better than a stock GTX 980. However, it chokes on anything that requires cpu->gpu bandwidth. D3D Bandwidth tells me my VM to SM and SM to VM speeds are only 1340 MB/s and 1282 MB/s respectively.

I thought it was a problem with the card, but other cards do the same thing in that slot (even my old 8800 Ultra runs at PCI-E x2 1.1). Therefor, I thought it was the motherboard (it came with a dead RAM channel as well, GIGABYTE G1 Gaming GA-Z170MX-Gaming 5) so I RMAed the motherboard and got a new one, an ASUS Z170M-PLUS.

The same problem persists after all Windows 7 updates, all driver updates, most recent bios installation, most recent GPU driver installation, making sure no power save was effecting PCI-E state, checking BIOS for all settings that could effect it (tried PCI-E slots set to legacy only and UEFI, no noted change), and am pretty much at my wit's end here.

Is there a chance it could be an issue with the processor somehow? It's all I can think of.

My system information is:
Windows 7 64 bit
16 gigs of DDR4, dual channel, at 3000 mhz
Core i5-6600 @ 3.3 ghz
480 gb SSD
EVGA Supernova 750W
MSI GTX 980

Any and all help is appreciated!

 

[rujoesmith]

Do you have the card plugged into the grey or black pci slot?

 

[Psylantwolf]

It is in the grey slot, the only true X16 slot. The black slot only runs X8. Oddly, when the card is in the black slot, it does run X8, not X2. This is what makes me think maybe something is wrong with the processor, perhaps? One PCI-E channel works as it should and the other does not? It is, for sure, not an issue with the motherboard, as this same problem has happened with two motherboards, both new.