IPod Video Sync Problems

I've searched for this for a while but have yet to find a solid answer. I have several videos that were converted over the years into MP4 or H.264, all of which synced to my former iPod 80GB just fine. Now I have a new 160 GB and some of them will and some of them won't (via auto syncing or drag and drop -- if dropping I get no errors, just the "+" sign over Device then nothing on release). I can't tell what the difference is between the ones that work and the others. For example...
Video 1 (WILL go to iPod): 21min23sec, 245mb, MPEG-4, 624x352, data rate 1469, total bit 1597, 29 frames/sec, audio 128k @ 48kHz
Video 2 (will NOT go to iPod): 42min40sec, 414mb, H.264, 624x352, rate 1203, total 1355, 29 frames/sec, audio 152k @ 44kHz
Video 3 (will NOT go to iPod): 27min37sec, 270mb, MPEG-4, 624x352, rate 1214, total 1366, 29 frames/sec, audio 152k @ 84kHz
The only difference I can see is the audio KBPS but I can't see that making enough difference to cause compatability issues. I know I can just use iTunes to convert for iPod but I want to keep these files high enough quality to be watchable on full screen without needing to have a HQ version and an iPod version of 2000+ videos.
Any insights on this? Thanks in advance.

Many of my encoded videos are at 127kbps. I actually got this issue resolved by re-encoding everything that wouldn't sync, but the funny thing is I didn't change any of the settings. Just re-encoded everything as is and suddenly they all synced. I don't get it...
On an unrelated topic, maybe someone can answer this question here so I don't have to start a new post:
When I am trying to auto-sync my iPod I am having trouble syncing selected shows. I set to "Automatically include ALL episodes of SELECTED SHOWS" then go through a show and select certain episodes. But they don't stay unchecked if I Apply settings or go to a different show (ie, if I only check Seasons 1 and 4 of Futurama then Apply changes OR move on to the show Simpsons, all Seasons 1-4 recheck themselves). Any ideas? Thanks

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