Ya, or even x4, but the problem is that it is showing x1, even after pushing the ? mark. That is what is concerning. It's most likely a seating issue.
I think that your seating issue explanation is the best one.
another theory is that the power supply is unable to power it so it's throttling the 7970.
and the idea that I had was that the motherboard was limiting the lanes available to the graphics card.