Im assuming you swapped the devices around between the ports? (Moving mouse, plugging joystick in where mouse works, etc)
Was your gamepad plugged in at that time aswell? Anything in the usb when it crashed couldve been toasted. Including the usb controller itself.. It's possible there was a small power flux (dunno how likely it is for just the usb to die in that scenario) that killed everything. Do you have a surgeprotector/ups for your system?