Files in MOV-Container missing, although MOV is self-containing

Hello everybody,
I've got a strange problem here. We are capturing MPEG4-Files with a camera and cutting those files with quicktime pro (so that we don't have do re-encode those files in order to gain time). The files consist of a few MPEG4-Movie-Sequences (that are copy/pasted from the original files) and a small Signation-MPEG4 from the harddisk. Then the files are saved as self-contained quicktime-files and transfered to another computer.
But a few files will not contain the signation, although the moviefiles from the camera are in the container.
Is there a difference in Quicktime if a file is added by drag'n'drop, by "Insert" or "add to movie"?
I can't reproduce the problem (it comes up on a Mac and on Win with Quicktime 7.1.3) and it scares me
Thank you very much, i would appreciate your help.
ruby77
Powerbook G4 Mac OS X (10.4.8)

Could it be a solution that the file is - during editing the video - "Saved As" a self containing movie... But afterwards, when the last file is insertet and when the video is finished just "Saved". Maybe if you save a video through "Save" (and not "Save as"), for new, added files just the references will be saved in a self contained-video.
Your thoughts?

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