Jonathan, you can't bounce output from a Quicktime Synth, as the internal object synth doesn't have pluggable outputs at all. Its output is hardwired to the soundcard, and you hear it but it's being processed outside of Logic. If you look closely, you'll notice no meter activity in the master outputs when you're playing that track by itself.
One way to bounce it would be if you solo'ed the quicktime tracks, and re-routed the computer's outputs back into Logic and recorded it as Audio. You might have to adjust a few milliseconds to compensate for the delay, but it should work fine for the most part.
I hope this helps.
Luis
http://www.musicvancouver.com