One thing you may want to look at is the way your symbols are being triggered on the timeline. For example: you have an image of a ball bouncing, it goes down then up over the course of 30 frames and you are playing the FLA at 15 FPS so it takes a full two seconds per "bounce". If you are then putting that symbol into another timeline (probably the main timeline) you need to give the instance of that symbol the full 30 frames to go through the bounce before it stops, but if you give it 31 frames or forget to put a stop() command on the last frame, the sequence will repeat before clearing the stage.
I would look at how you have positioned the object that is being looped in the main timeline and remember that with each keyframe you add to the timeline the animation will restart from the beginning. Imagine the bouncing ball graphic is a video clip of a ball bouncing and not a collection of vectors being repositioned on the stage. Every time you have a keyframe on the symbol of the video on the main timeline, the video restarts and appears to loop. The same may be happening with your animation on the timeline.
Hope this helps.