1) Update the BIOS ( it should be the 990fxa gd65
2) Update the AMD chipset driver too, the chipset driver comes with the pcie controller driver, that will make sure there is not the driver problem. http://support.amd.com/en-us/download/chipset?os=Windows%208%20-%2032
After that, if the pciex16 still shows as x1 under load, because the gpu may run power saving mode in idle, you may try use the cpu-z too. Otherwise the MB has problem.