First make sure that MWS was installed to the default location. That is:
c:\program files\magic workstation
If that was done correctly, next make sure that when Version 3.1 was run, you chose to overwrite the file "warcraft.mwbase". The base file links all the sets together. If the master base was not updated, simply download the masterbase file from the front page, run the .exe file and choose to overwrite the old "warcraft.mwbase" file. That should fix everything
Must get ready for Conts... (sounds much worse than Nats... lol) - Northern General