I use Another GUI as Sean mentions too, but i sometimes also get the extra frames in the end of the ProRes file so i dont use it much.
Another an new thing to consider is this QT codec:
$50 for a true QT codec that makes it possible to make ProRes directly from AE, AME and Premiere. I have not yet bought it, but it seems like good solution, hopefully without any issues :-)
But more and more windows apps are getting ProRes support (Assimilate Scratch just announced it for v8) so maybe Apple is getting more relaxed with the license.