I never actually looked into GPU-Z as never saw some performance issues, but once started it saw that my MSI GTX660 runnig PCI-E 2.0@x8 though both GPU both mobo witch is GA-Z68X-UD3H-B3 (rev. 1.0) supports PCI Gen3. GPU-Z also says card supports PCI-E 2.0@x16 but not 3.0
GPU is mounted in the x16 driver is fresh 320.49
Same info shown in Nvidia system information.. Tried to check BIOS for setup that could influence this but have not found anything.
BTW mobo says gen 3, but depend on CPU in my case 2.0:
The GIGABYTE motherboard is fully configured to provide gamers with the latest Gen.3 PCI Express technology, delivering maximum data bandwidth for forthcoming discrete graphics cards.
* PCIe Gen. 3 is dependent on CPU and expansion card compatibility.