It's definitely not the motherboard. I just ripped out a Frontside connectors from my old Pentium 4 and hooked it in, booted it up and shoved in a USB drive.
Everything worked fine.
I think it might be that the pins on the opposite end of the the cable on the case are not hooked up correctly, though it may be a little difficult getting to them without doing damage to the case. I will update.