I had the same problem. The USB ports did not work, and other ports did not work. I simply fixed it by replacing my mother board with another one.
Just get your motherboard replaced and see if that fixes your problem.
He should try the most simple explanations first.
OP: There is a wire that hooks into the USB connector port, locate the wire from your case - it should be easy to find - and make sure it is plugged into your USB connector ports. The ports exist between FDD connector and your SATA connectors.
If already connected, try uplugging and plugging into a different USB connector port and/or double check that it is firmly and correctly placed.
I do not recommend taking Michaels advice by RMAing your motherboard when the most likely explanation is the case has faulty wiring. It is most likely the case, it it turns out to be a connection problem.
Edit: Oh, it is your back ports, not your front ports...In that case, I would double check your wiring and make sure everything is snug and secure. Are you using onboard VGA?