I have had issues like this before where the swf works fine by itself but when you call it externally from another swf it looses its functionality. Just a thought on this I know it worked once for me. Try checking your code to see if it matches with the new code in other words
say this is the original code
Code:
ExternalClip_MC.OldMovieClip_MC.gotoAndPlay(2);
new code would be something like this
Code:
NewMovieClip.ExternalClip_MC.OldMovieClip_MC.gotoAndPlay(2);
Just a thought I know it worked once for me. wont hurt to try just make sure you save your previos version.