Look for a feature in the bios called EUP. On many boards this powers down USB ports(and just about everything to get the power consumption under 0.5 watts) when the system is off.
What board is it?
EUP description from ASRockhttp://www.asrock.com/feature/EuP/index.asp
Some older boards used to have an option to take usb power from the 5v standby(so the power was always on) on the power supply, but they all do this now for the most part. still may be worth a look. Used to be a jumper near the usb ports on the board it self.