AFAIK, the AVI container was never capable of handling variable framerate. So the indexing of the video for that container is likely different. I am not sure about your questions on audio. I have never done anything other than transcode the audio between formats. I have never dealt with stretching or compressing duration. I know that you have to deal with the pitch change then, but I don't know a lot about it other than what I have read on sites like videohelp.com or doom9.org. From reading, it seems like a non-trivial exercise.