Is what I got for my files that go into iTunes that are .mp4 and have .mp4 extension.
Truly strange that they work on my Mac and not yours.
The only conclusion I can come to is there is something in the original files encoding that is ignored by handbrake but not iTunes??
I know the reason why… 
Or I have areal good guess
SO I tested and tested and tested and it always failed unless the extension was m4v. So then I was working on creating a error catching part of the script, and thought well, to force iTunes to reject the file I will use mp4.
iTunes DID NOT Reject the file. SO I now had a video that was mp4 and iTunes did accept it… :mad:
More investigation…:rolleyes:
Now I think I have it. If the file has A52 audio (5.1 DD) then the file needs to be m4v. I have tried on 3 different files. If the video has a 5.1 Audio track and I try to add it as mp4 it fails. Videos with Stereo/MP3 Audio can have the extension mp4
Please let me know if you discover the same.