Are these USB ports used for attaching drives - any type, hard, optical, flash?
If so do you always use the "Safely remove hardware" facility provided in Windows?
The effect you describe seems very much like that which you get when the port has been destroyed by removing hardware in the incorrect way i.e. just unplugging it rather than going through the right procedure.
USB may well be plug 'n' play but it certainly is not UNplug 'n' play and it is easy to wreck the port connection, the USB device (or both) by using the incorrect connect/disconnect method.