I do believe that the changes you are making in the Program Files folder when you're installing mods are contributing to the problem. It is a very complex thing to explain what Vista is doing with Virtual Store (and why it's doing that), but let's just say that Vista doesn't like you messing with any files that are contained in the Program Files folder. Depending on how you're making the changes, and how often, I can very well imagine that Vista could determine that there is a security risk and shut down the game.