Try putting your whole scene into a movieclip.
Or if it's possible, split your movie into parts and put those into movieclips. Don't forget to use _root.play() and _root.stop() inside the movieclips.
Why?
_root.stop() = makes the main timeline stop, but the movieclip keeps playing.
_root.play() = makes the main timeline play.
Hope this helps.
It may be exhausting, but it's effective.