I've only tried this once, but it worked like a charm on a Quicktime file otherwise unrecognizable by Windows.
I think you are going to love this--a freeware transcoder for Quicktime and AVI!
http://www.squared5.com/svideo/mpeg-streamclip-win.html
Streamclip
Moderators: Víctor Paredes, Belgarath, slowtiger