Things to check:
I've seen boards where something in the BIOS is disabled but Windows can still detect it. Worth checking.
I'd also try temporarily disconnecting any of the case USB ports from the motherboard and just use the built-in ports. If there is a bad or shorted wire somewhere it could be messing up the whole works.
Have you run the Intel driver updater?
You could also try downloading a bootable version of a Linux distro and see if the USB works with that. If it does then we know the board is OK and it's a Windows problem.