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