ASUS Z97-A stuck at 3.0 x2 speeds (980ti)

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CPU - i5 4690k, 4x4GB ram,
980 ti stuck at x2 PCI-E speeds w/ asus z97-a motherboard. I have tried flashing to earlier BIOS, reseat GPU, and reset CMOS. help plz
 
I took my motherboard out the case and tested the other PCI slots, along with testing it with no external devices at all. All of this with after removing as much RAM as possible, re-seating the CPU, and wiping the drivers.
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I have a friend who is going to test my gpu for me, so hopefully I can soon get this sorted out.
 
One of the PCIe slots is supposed to be PCIe x2, though I don't know why the card would run at a lower connection on the other two PCIe x16 slots. Are you testing the card in a game or idle? When you aren't playing a game or some other graphically intense workload, the card will sometimes use fewer lanes and/or a lower PCIe version to save power.
 
I saw this in the BIOS, and I did a bandwidth benchmark for the PCI bus. The score was extremely low, at around 2000MB/s. I also checked it with GPU-Z, doing the render test. Still at 2x speed.
I checked the CPU pins, and the motherboard for any obvious shorting. No signs of anything wrong.
 
It's the card. I tested an artifacting, old GT 8800, and that showed up as 8x PCI-E, while the 980 ti was still at 2x. I have installed the accelero xtreme III to it, and the problem did arise before (I didn't care). I'm going to the US during June/July, I guess I'll RMA it there.