Okay... I know I said I wasn't going to use QuickTime Pro anymore but here goes...
Making 640x480 iPod Video with QuickTime Pro has become very easy since I learned how to import elementary streams.
Tools: MPEG Streamclip and QuickTime Pro with the MPEG-2 Playback Component.
1. Rip DVD.
2. Use MPEG Streamclip to demux to m2v and aiff.
3. Right-click on m2v and select 'Open With QuickTime Player' (large video files may take a while to open)
4. Play movie for a few seconds and make sure audio plays and is in sync.
5. Select 'File' > 'Export' > 'Movie to iPod' > 'Save'.
It took about 4.5 hours to encode 'A Nightmare On Elm Street' and, as I have said before, the results are amazing!
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As you can see I have re-edited my post (again).
It seems that the problem I was having had to do with my iPod and (hopefully) not the method I described above.
After I reset my iPod, all of my videos play very well... including those converted as described.
Sorry for any confusion,
Nice post! I'm going to try that if it will work for me...