Crissy that is not stuipd nore silly to wonder in the least and it is one of the first things to check in the trouble shooting process when you turn from the device itself to the system
I would probably delete everything in the Hadrware list dealing with USB and reboot so windows will find new hardware and reinstall things how it wants them to be installed (resources and such) and I would also look in the admin logs to see if anything untold took place right before the mouse quit working if this is Windows XP. If Windows 98 I would run Computer Information in the Accessories/System Utils to see what it returned to make sure it actually sees the port in question...
Spikes and such, devices, such as DC mentioned can also zap the sysem and cause windows to loose site of devices at odd moments...