Unless I am mistaken, Flash renders the video file as a series of frames, like one image (per frame), one after the other. The rendering does not include any changes that are only created by actionscript. Sort of like, if you don't see the change displayed in the frame, it does not get recorded as part of the video.
I've also had some part of Flash not render as .avi, so it's not perfect for that. I'd be curious.. if you go to one of the problem areas and scrub the timeline to a frame (in the Flash timeline) and export an image of that frame, is the image correctly displayed or does it have the same issues as the .avi?
Good luck,
EfV