Were these second level animations triggered by actionscript? If that is the problem then you may need to play your Flash files and use a screen recorder to capture all of the animation.
I didn't use any Actionscript whatsoever (can't get the hang of it).
I only used symbols and tweens, of all 3 types.
Do you get any errors when you test the movie in Flash? You say that you have several bits, are these seperate Flash files? Is the problem always in the same place when you export to Quicktime?
Never mind, the mov files seemed to have fixed themselves when I exported them again.
But to answer your question; yes, I used several individual flash files and planned to compile them together.
The errors also occurred in the same place each time, but there were no flaws in the swf files when I looked at them by themselves (without importing to After Effects or anything)