I assume you have changed BIOS, Peripherals > PCH from Auto to x4, saved, restarted, boot to OS, then restart again and change back to Auto, save and restart? I know
, CMOS reset should take care of this.
If you don't have something installed in the other PCIe slots that might effect something like this I can't think of any reason why a single x16 card would only run at x4 in the x16 slot.
What are the specs of your CPU and Memory? If its working elsewhere, it sounds like some type of compatibility issue. Maybe someone else has some ideas?