Trying to research your problem to help you...
1. Have you tried re-seating the card in the PCIe slot?
2. Have you gone into bios and made sure that your PCIe slot is set to be read first and that it is set to Gen3 (PCIe 3.0). I don't know if this will work but it can't hurt to try.
3. ***Apparently you have a PCIe slot configuration setting in bios. Please make sure this is correct. Check page 55 in the downloadable manual on Gigabyte website.
4. Run Valley Benchmark or game in windowed mode and look at GPU-z. See if it changes to x16.
Possible solutions to try last...
1. Try updating bios to latest if it isn't already
2. Try re-seating CPU
EDIT: Did you install the proper INF file for your chipset?