[Meads]

In order to achieve correct playback after the bounce you'd have to route the discrete tracks within Quicktime correctly, and even then you cannot be sure, that it's working properly (from my experience).
If you want a QT with 5.1 audio, I'd advise you to create an AC3 stream of your 5.1 mix, and paste this to your movie in Quicktime Pro (using Perian).

When I'm bouncing to Quicktime in PT, I always make a stereo downmix first. That's the only way to create a properly working video file, that you don't have to worry about, when you send it to clients or whatever.

Edit:
BTW, thanks to the Downmixer plugin that comes with PT10 you don't even have to make a stereo mixdown anymore. Just insert the Downmixer on the 5.1-track you want to bounce, load a preset, route the track to a stereo output and go.