Video's Sounds Stops Periodically
I don't know if this has been covered in another topic, but I'll try my best to answer your query.
I'm assuming that you:
1) Have a 60GB iPod with video
2) Have upgraded the firmware on it to 1.1 using the 2006-01-10 Updater
Ok, this issue where your video files stop, or the sound stops periodically onlly seems to be affecting users who meet the above criteria.
The only way I have know of to stop the pauses, is to run your video files through Quicktime Pro and choose "Export" from the file menu.
Once the Save as dialog box appears, set the export type to "Movie to MPEG-4" and then press the options button.
Once the options appear, choose "Pass Through" from the Video Format drop-down box, and then do the same for the audio too...choose "Pass Through"
Then export the file to a directory of your choice and then drag and drop your new file into iTunes or directly onto the iPod icon in iTunes.
I have found this to work, and so far the largest video file i have is over 1GB.
I'm sorry but I'm unable to help with your H.264 issue, as I'm not that savvy! Most of the info I've found out has been by trawling the net!