The chipset driver does control the pcie, memory, and other components, that why I suggest to try update the driver to see the PC can recognize the GPU or not after the update, also sometime you update the BIOS then you can solve the problem too, but your MB looks like new model, you don't need the BIOS update.
So if there is not the software problem, that it is the hardware problem, and I think you can't fit the hardware problem, so either return it or use the pciex8 for the gtx650. If you use single gtx650, and you will not see the big different performance between pciex16 or pciex8, reviews.
http://www.pugetsystems.com/labs/articles/Impact-of-PCI-E-Speed-on-Gaming-Performance-518/...