When you say you had Works 6.0 installed and upgraded to 2000, I suppose you are referring to the program Word, which usually is part of the WorksSuite.
In my experience the Works and Office versions of Word often cause these kind of conflicts, up to the point where Word just refuses to start. Reinstalling the application usually does not help.
First try to find and rename the file Normal.dot, and restart Word. A new file will be created and the problem may be fixed.
If not, then the more agressive approach is to start Regedit, find the key HCU\Software\Microsoft\Office\9.0 and rename it to something like Dummy9.0. Then reinstall Word 2000 and hope of a miracle. If so, you can delete the renamed key and continue.
If not, then I do not know any other resolution than to format and reinstall Windows.
This problem is, by the way, just as common in WinXP as it is in older versions.