What is the source material, how is it interpreted in AE and what are your render settings. Things looking choppy is the classical symptom of fields being inversed/ ignored/ lost somewhere in the chain, when they should be retained, or forcibly introduced into progressive footage. Most likely your choppiness is simply doubled frames in those areas because of the aforementioned mishandling of files.
SOURCE MATERIAL: an .MPG from a digital camera. it says field order is progressive, fps-30, 640x480, pixel aspect ratio-1, audio is 32000 compressed bit rate, mono channel.
i'm importing the file as FOOTAGE, and when i render i'm using all best settings: quality, res, everything else at current settings. i AM stretching the video a bit in the program (from 640x480 - 800x600), and then rending it at these dimensions. my output module is just quicktime using a MPEG-4 compressions codec at highest quality. audio is made to 48.000 16bit stereo...
...as i write this i'm wondering if my stretching the video in program and rendering the audio at a higher bitrate then it is would mess things up? the audio in this thing is out of sync as well.
Well, most MPG in digital photo cameras is some sort of MPEG-4, often deviating considerably from standardized specs, so anything is possible. In your case, a look in the manual might offer some insights. I'm beggining to think that the clips are actually recorded at a lower frame rate (e.g. 24fps) and then use some sort of pulldown to look like 30fps. that#s not noticable when just viewing them, but gets you when editing. they may require to have the pulldown removed by interpreting them as 24fps pa. likewise, 30fps and 29.97fps are different things in AE's world, so that should be checked as well. Those discrepancies could also well explain your audio issues. The scaling should be unrealted, as AE works on fully reconstructed frames, not the source stream. It just cannot reconstruct the frames correctly in the transition areas, that's why it looks so weird.