Compressing video for iPod using QuickTime 7 Pro ("expert")

Hi all,
I purchased QuickTime 7 Pro thinking I would be able to compress 640x480 H.264 video for an iPod. I have a specific application that requires precise control over the compression -- that is, the no-option "Movie to iPod" export setting ain't gonna cut it.
I have tried many, many different setting combinations using "Movie to MPEG-4" and "Movie to QuickTime Movie" under "File" --> "Export" in QuickTime, and I have been careful to limit sizes and bitrates per iPod tech specs as published on the Apple Web site. However, while all of the H.264 files I have output will open in iTunes, none of them will sync to my iPod. Videos I output using standard MPEG-4 compression will sync to my iPod (and look awful), but videos using H.264 will not.
Does anyone know what settings I can use to export 640x480 H.264 video to my iPod, and how I can have more control over the process than just "Movie to iPod?"
Thanks!
-- Joey
What I got (the technical details):
WinXP Pro with all the latest updates on Intel
5G 60GB iPod w/ firmware ver 1.2
QuickTime 7.1.3 Pro
iTunes 7.0.1.8
multiple Wintel machines   Windows XP Pro  

Welcome to the discussions, Joeysirmons.
The developer that created VisualHub (Only for the Mac) has discovered how to create iPod compatible 640x480 video where the user has full control over the compression. The changes he made were to some public libraries so these methods should be finding their way to the ffmpeg based tools for Windows soon.

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