What the!? Are people avoiding clip compiling questions or something?
you're not likely to get much help because the flash components are known to cause many problems and almost certainly have been developed by coders with more experience than you. so, it's no surprise and not very interesting that you're having problems with your components.
also, there's not much anyone that's interested could do to help you. they would need to decompile all the compiled clips to see which are causing the conflict(s) and that would be a lot of work and very time consuming unless you only had a few lines of code total in the clips that conflict.
Waittaminute, waittaminute. You said that they would decompile the compiled clips to look for problems in code.... but I'm telling you that there is little to no code in these clips and any code used so far is for animation only; they are simple lines in the top layer of each clip. They will work fine if there is only one compiled clip, but will sometimes not work if there are several.
So in essence you're telling me that nobody here knows even one alternative to working with large movies, or clips? Am I to pity this forum or the developers, because that seems a little unreasonable.
don't worry about it. you'll get lots of help. just be patient.