Are all motherboards running the most recent bios version?
Check GIGABYTE Latest Beta BIOS to see if there is a newer beta bios available for each motherboard.
Did you install the usb 3.0 drivers from the motherboard CD?
Have you checked to see if there is a newer usb 3.0 driver available from Gigabyte or the usb OEM web site?
When you removed the old Nvidia drivers, did you also use Driver Sweeper to remove any remaining Nvidia leftovers?
Did you download and install the correct Geforce driver versions for your operating system and video card?
Sometimes a specific driver version has issues with some video cards.
Try download a slightly older Nvidia driver version and see if the problem remains.