Can't import mp4 file into iTunes

I have had a lot of success converting my DVDs to mp4s and storing them on external hard drives to play through AppleTV (I love AppleTV!). However I have a couple of files that will not load into iTunes. I get no error message but when I try to open with Quicktime I get an error message saying the file is not a movie file. The files I am having problems with were recorded from cable tv and written to DVD. Please help...

HOCKEY PUCK! Looks like this isn't a solution anyway. Tried it on a 250 MB file with 7 chapter markers and got some very random results.
1) Clipped the previously embeded graphic from the iTunes file and applied the same workflow. This time it did not save the chapter track (just like it does in MPEG Streamclip).
2) A bit confused, I deleted the newly created file and tried again only without clipping the graphic first. This time when I attempted to open the newly created file there was not video track whatsoever.
3) Now I'm getting really confused. So I delete the new "audio" file and load the source file one more time. This time, instead of relying on the the "current default" options (i.e., the ones last used), I open the options window and find the "Pass through" has reset to "None." So I attempt to change it back to "Pass through" and guess what... Now that option is "grayed out" just as you say (and as I believe it used to be in QT v7.1.3).
4) Totally flabbergasted, I close the player and load a secondary file (paired TV episode to the first file) and open the "Movie to MPEG-4" Export option. To my surprise, the audio and video "Pass through" settings are back again. Okay, so this time I decide to "tic" the chapter track to see if that will prevent it's loss. No joy!
Basically, I spend a few more wasted hours trying to figure out why I could not duplicate my original success. I even drag out other applications like SimpleMovieX and MPEG Streamclip which have "Save As..." options to "compatible" containers. Both delete the chapter track just as QT Pro is currently doing. Suffice it to say I'm growing angrier by the moment and finally decide to quit so I can update the latest results here. Sorry everyone... Really thought the latest QT upgrade had someting going for itself here. Looks like I merely "jumped the gun" instead.

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