pyradyn: The problem is probably files being left behind when you uninstall, so they are still there and causing problems when you re-install. Try this: Uninstall RTW, then find the game folder (probably C:\Program Files\Activision\Rome - Total War\) and delete it. Then re-install RTW, patch, etc.

Before you delete the game folder you might want to make a copy of saved games, and preferences.