Okay, so let me get this straight.
You have one symbol instance that contains about twenty layers of movie clips. Most of those movie clips contain half a dozen movie clip layers of their own.
Am I getting this right? If so, whoa.
That would be so far removed from the way that I construct my videos that I could offer you no real constructive advice regarding how to proceed. The method of animating scenes within movie clips is well known and used by such authors as Proxicide and Suroy, but I don't use it. If I had to guess, I would say that the method that you are using is putting great stress on the flash program. Again, I could be wrong. I'm not familiar enough with the technique to provide a definite diagnosis.
The only immediate observation that I can offer you is one that I have heard, but not been able to verify. When I was learning flash, I was taught that the flash program might have problems with library items that start with a capital letter. I have never been able to verify this, but every item that I import and every symbol I make begins with a lowercase letter all the same. I'm not saying that's your problem, I'm just saying that it might be worth noting.
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You said,
"when changing how the character is standing, if I were to have made the character bigger in the previous key frame, I would not be able to match the same size in the new position very well if it were placed in the _root timeline, as I would have to eyeball it. (IE The character was standing, but scaled up to make him appear larger, and then goes into a walking animation or vice versa)."
This is a problem that you can clear up before you start by taking all of your bitmap instances from a character and placing them into one keyframe like a spritesheet. Once they are all in place, you can group them all together and then scale the group to whatever size you like. Then, you ungroup them and start converting them to symbols in their newly-resized state. It's probably a bit late for you to do that now, though.
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You also said,
"For zooming I've been manually increasing and decreasing the size of the symbol (containing all the animation of the character used for the entire scene) using key frames. When the character isn't supposed to be visible in a specific section of the scene, inside the symbol I simply enter a blank key frame and then add another key frame where the character is visible again (this is all done inside the "scene symbol")."
You can eliminate this entire zooming-resizing issue by using a V-CAM. If you have a VCAM in your scene, you can "zoom in" by simply scaling the V-CAM to make it smaller. It is easier on the flash program because you are manipulating one object to get this effect rather than resizing dozens of things. Again, that is something best worked out before you begin, and probably not at the advanced stage that you are in now.
I wish I could be more helpful.
R1665