Yeah, I agree with you, brash. I always use MPEG Streamclip for splitting 5.1 tracks. You just have to make sure to label the stems correctly when you save them, so you don't mix up which channel is which later.
As a sidenote, I finally got Final Cut Studio 3. I've been messing with it all afternoon - I like Avid better for editing a movie from scratch, but Final Cut lends itself much better to fan editing.