This is something I've hit a few times across several projects. At some unknown event, animated movie clips will start flickering, like if you have a character the head will start to disappear on or off. Once one clip is broken, EVERY animation across the Fla will have flickering issues. Like simple tweens will show the first few frames, cut out completely then show the last.
Not sure how this is caused, guessing it's more frequent if your merging Fla's. The only solutions I've found is
1) From Evan (thanks!): finding the offending animation in the Fla, just open the symbol up in the editor, close symbol...somehow this corrects things!
2) going through animation by animation and trying them out in a separate Fla. Finding the one that flickers, and deleting it and replacing it with a backup will correct...the entire file!
3) In one case this was due to an invisible textfield (imported from Illustrator) that acted as a landmine, once it was removed everything worked fine. I found it using the MovieClip Explorer for all textfields, looking for ones that didn't belong.
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Another fix, is to open every flickering symbol. Once you open a flickering one, it will repair. I just did it to 300 symbols. Painful, but it works.
I’ve noticed the problem with legacy content that we are now editing in CS3. It didn’t happen in Flash 8 but it will happen with animations we built in F8 that we are now editing in CS3.
I’ve seen this happen in Flash MX2004 as well, though. I see it happen more often when you have a larger library for sure.