section of your BIOS for a "standby" option.

Just a side note, the power to the mobo NEVER goes fully off because a 5 volt standby voltage remains applied, however, that is not your problem because the power supply would normally appear to be off and the front panel light would be off.

Tell us the nature of the incomplete shutdown, anything on the monitor screen? If there was then it could be one of the normal Win XP shutdown issues.

The USB ports actually can provide 5 volts to power devices plugged into the USB port. However the current available can be very limited in some systems. Possibly the feed on your mobo to the USB got zapped. Possibly related is the failure to shutdown the power supply, and that could also be a mobo problem. With ATX power supplies the logic circuit on the mobo is what actually turns the main power supply rails [main 5 volts, 3.3.volts, and 12 volts] ON and OFF.

If it twere only the USB power problem, a simple solution would be to buy a Powered USB hub external to the computer. The powered type have an adapter that you plug into the AC power and it will provide the five volts to the devices connected to the hubs output ports. They can provide much more current to devices.