Audio dropouts when converting dvd's to ipod video

Love my new 60 Gb iPod in black!
I have been able to successfully transfer several of my DVD's to my iPod using handbrake. Such movies as, "The Big Lebowski" and several episodes of "Bugs Bunny", music videos from a "Best of Blur" DVD, all transfer seamlessly (in the destination box of handbrake, I select MP4 file, then when the transfer is complete, I ammend the end of the file to m4v before dragging it over the itunes icon in the dock.).
In any event, for some reason, several other DVD's I've tried to convert using the same method (R.E.M. Roadmovie, Queen - Live at Wembley Stadium), reveal dropouts in the audio (video keeps playing without a glitch). Dropouts last for no more than a second and seem to occur between every 30 to 50 seconds. These same DVD's play flawlessly in the computer and home dvd players with no signs of dropouts. Any ideas, suggestions would be greatly appreciated concerning how I can get rid of these dastardly dropouts.
Thanks,
Pete

Hi Rick,
I am extracting the material from the dvd directly using handbrake. The file that handbrake creates lands on the desktop. I then ammend the end of the filename from mp4 to m4v. Following this I click and drag the file onto the itunes icon in the dock. I can then download it to the ipod no problem. The dropouts occur no matter where I play the file. In other words, on the desktop (with QT), in the itunes library and on the pod.
I went back and looked at all the dvd's that are giving me this trouble. The culprit seems to be that the audio signal is in LPCM (linear pulse code modulation). Just for the **** of it, I tried to rip one track using handbrake changing the sampling rate of the audio to 48,000 Hz which I believe is what LPCM uses (previously I had set it at 41,000 Hz in handbrake). But no go, still has dropouts. One of these problem dvd's has a second audio option in AC3 (2ch). As a test, I ripped one song using that. Dropouts are gone. However, the audio is a director's commentary (on the music video he shot) with the music in the background, so it's not what I want.
Is there any way to convert LPCM to AC3? Or any other way to fix this dropout problem.
Thanks,
Pete

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