Based on the number of tests performed on your system, I'd next recommend clearing the CMOS; see the following URL for the step-by-step instructions:
Note: Make sure you leave the CMOS battery out for 20 min., at least.
Otherwise, I'd recommend contacting our Tech Support Dpt. with your system handy for online troubleshooting:
Are the USB connections you refer to in the case or on the mother board , If you are talking about your case connections you may have a bad ground??