Have anyone opened up your Eee PCs at all for anything? If so, the cable the connects the the USB + Audio board to the MB may have become unattached or broken. I upgraded the RAM in my Eee 1025CE which required me to fully take the laptop apart and when I was reconnecting everything I didn't quite put the ribbon cable properly back that connected audio board and USB board.
Anyway, just thought I was would put it out there as it could be a hardware issue, not a software issues.