Upgrading to MovableType 3.2 was an ordeal. Whenever trying to open up mt.cgi to upgrade the databases, etc, I kept getting the following error:
CGI Error - The specified CGI application misbehaved by not returning a complete set of HTTP headers.
Researching the issue, I came across the following post:
http://www.sixapart.com/movabletype/beta/2005/07/user-to-user_be.html#c5783
Following the instructions listed in that post by JoelD, everything is working fine and dandy on my Windows 2003 server.