When you export to .mov - what settings do you use?
I suspect that part of you app is a pure ActionScript - thus, in Export Settings >> Stop exporting you need to check After time elapsed radio button and enter for how long movie will play.
I have tried using a number of different codecs such as animation codec, intermediate codec, etc. I have tried checking the after time elapsed radio button. I've also tried exporting as a png sequence. It's not like it stops halfway through exporting; it gets to the end and most of the animation is there it's just that certain elements (such as embedded flv's) are missing from the exported sequence.
Just tried it with flv embedded on timeline and it worked perfectly. I am on PC though. It is difficult to tell what is going on without knowing more about how your timeline is organized.