ok
1.  have you tried running the games uninstall from the start menu?  I think run the PTW uninstall, then the Civ3 uninstall.  
2.  reinstall Civ3.  Reinstall PTW.  Download patch 1.04.  Perhaps even if the game doesn't uninstall, a reinstall would overwrite the bad parts.
If that stuff doesn't work, go to the dos prompt and type format c:
just kidding of course, please don't do that!  if that doesn't work, check back here.  

  good luck, I've had more than my fair share of glitches with computers