HD movies good in iTunes/Front Row, not on Apple TV :(

I have a library of 100+ HD movies, all of which play fine on my MacBook with 2GB RAM. Out of the group, only 30 show up on the Apple TV, and of those, only 4 play audio along with the video.
Any ideas?
Setup:
- Apple TV 40GB, current software
- Connected to Panasonic plasma via component & analog audio
- Late 2007 MacBook, 10.5.6, 2GB RAM
- iTunes 8.whatever, the latest
- iTunes library stored on external 1TB WD MyBook

Happy to report after much trial-and-error, I've been able to convert 80% of my videos using Handbrake (as MKVs, MOVs, and M4Vs). Here's the specs for those who are interested:
OUTPUT SETTINGS
- Format: MP4 file
- Large file size (checked)
VIDEO
- Video Codec: H.264 (x264)
- FPS: 23.98 (NTSC Film)
- Average Bitrate: 4500 kbps
PICTURE SETTINGS
- Output: 1280 x (whatever height)
- Keep Aspect Ratio (checked)
- Anamorphic: None
AUDIO & SUBTITLES
Track 1
- Audio Codec: AAC (faac)
- Mixdown: Dolby ProLogic II
- Samplerate: Automatic
- Bitrate: 160 kbps
Track 2
- Audio Codec: AC3 Passthru
- Mixdown: AC3 Passthru

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