How can I insert the mysterious iPod Atom to make a movie iPod friendly?

Hello. I've been looking for an answer to this problem all over the Internet and haven't found anything! An Quicktime GURU out there?
THE PROBLEM:
I have several mp4 video files that iTunes won't sync to my iPod. They play well on QT, FrontRow and iTunes but then iTunes says "This video cannot be played on this iPod".
Yes! you know that message too...
We all have gotten that message before, even when we know the video will play perfectly on the iPod because it was encoded on H.264, AAC, etc, etc...
Doing a little research I came to the fact that the problem is that these videos are missing an "iPod Atom Tag" which tells iTunes that the video can actually be played on the iPod. Seems quite simple but wait, there is a catch...
Nobody knows how to insert this iPod Atom in the mp4 file!!!
I found a nice UNIX app called AtomicParsley which let's you edit these tags but then I'm missing the important information... The iPod Tag code and the value which is supposed to be set to...
THE QUESTIONS:
Does anyone here has any idea on how to push the iPod Atom inside the mp4 file? Will AtomicParsley do the job?
Which is the code of the iPod Atom? Is it uuid?
Which value should I assign to it?
Is there anything else I have to do to the files to make them iPod friendly?
Most people would say that the easiest way is to use Quicktime Pro to re-encode the files but then the files grow in size, they loose some quality and features and not to mention that it takes forever to re-encode them again...
I believe that this app, AtomicParsley can do the job if I know which tags to modify and the values I should set them to but that's the information I'm missing...
I would really appreciate if someone can point me into the right direction and give me a little help with this matter. Thank you very much!
Alejandro Cordero
Costa Rica.

I appreciate your comment but I guess you didn't exactly understand my problem...
Handbrake is a program that extracts the video from DVDs and encode it into a movie file, usually mp4 files like the ones I need to fix. It won't work with movie files that you already have on your computer.
Here is the deal again:
1 - I have mp4 files in my HD. I am not encoding from my DVDs.
2 - AtomicParsley is a program that can insert atoms in an mp4 file and it only takes a few seconds to do it and the movie itself remains untouched. I believe this tool will work fine but...
3 - I just need to know what to tell to AtomicParsley. That is the iPod Atom code which I think is "uuid" and the value it must have which I really have no idea... :P
Using this tool will insert the atom in a few seconds so I don't have to re-encode everything from scratch. Each encoding takes a few hours for a whole movie. Why spend many many hours re-encoding when you can solve the problem in a few minutes...
Again, thank you for your comment. I'll keep waiting for an answer and keep the re-encoding option as a last resource.
Alec.

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