As far as I know, your waypoints are stored in a file named GARMIN_WPT.NVM stored at Documents and Settings\<your name>\Application Data\GARMIN\GarminMobilePC. Copy that to another location plus the file current.gpx in the GPX folder at the same location.
Assuming you have the hardware version of Mobile PC meaning the package included a GPS (20x or 10x), you can then delete that folder after uninstalling the program. A new install will rebuild the folder and may solve your issues. If not also delete the 'Devices' folder at the Garmin folder location and try again.
You can then restore your current.gpx file to the new GPX folder and the waypoints should be rebuilt. If not, restore the GARMIN_WPT.nvm file to its folder.
If you have the software version of Mobile PC, this is not a good strategy as you will lose the license for the program.
Terry