i had this problem while i was making option buttons to mute sound and music separately, and when the music was turned off only one sound effect would play and the sounds would be delayed, i fixed it by using setVolume() for the music.
What rynad said actually applies to a broader aspect - on more than one occasion I've had a project where a movie didn't behave the same when comparing between the in-flash test, and as standalone swf.
As for your problem specifically... I;m just brainstorming here, but could it be that you've added more code which has to run every frame? Perhaps the movie wants to execute too much at the same time... Like I said, it's just a guess, and if it is indeed the case I don't know a quick solution to it...