Finally, Six Apart got back to me with a fix. Under their new fix, I did not have to involve my hosting provider. They gave me a customized Bootstrap.pm, and required me to create an IIS virtual directory. It was a much more elegant solution than the one they gave me on the first try, and it actualy worked, so that was pretty cool. It has something to do with IIS not setting the working directory for cgi correctly.
So onward with Movable Type 3.2!