ITunes mutilated my video files

I had a serious issue when I tried to tag several movie files as "TV Show". iTunes kept spinning while the Info/Tagging window was open, and when I eventually cancelled its attempt, I found out that it had somehow destroyed the original files.
They were there, but they would no longer play in iTunes, AND IT WAS NO LONGER PLAYABLE anywhere on my computer, or re-convertible. I don't know what iTunes did to those videos, but it mutilated them.
Luckily I had the "originals" - eg the versions that weren't initially ipod compatible (such as .avi and .flvs and stuff) so I just ran them all through VisualHub again, after deleting the mutilated files. That was annoying because it takes quite a bit of time to do nice 2-pass H.264 conversions even on a MacBook Pro.
The second time I (a) did not attempt to tag the files, and (b) made duplicates of them onto another drive as a back-up. So far things are fine, but it's annoying not being able to organise my movies more efficiently. Especially as video playlists don't seem to load on the iPod Touch - AND, as the Apple Help notes - there is currently a bug with video Smart Playlists not working at all (they won't save).
Love my iPod, but its software/OS has some way to go. Roll on Februrary

Well the other person has witnessed this behaviour - in that it took several minutes.
I cannot see how it could NOT have been iTunes (coupled with my cancelling its tagging process early) that mutilated my files. What else could have done it? All the other movie files, that I did not attempt to tag, or that I tagged as Music Videos, were fine. All these files were identical in their codecs and conversion parameters.
I have managed to repeat the error today, with a test file. The file goes to TV Shows, but is not playable. Trying to play it outside iTunes with QuickTime generates the error:
"The movie could not be opened.
"An invalid public movie atom was found in the movie."
Trying to open it with software such as MPEG Streamclip (which will sometimes even open damaged files), gives the error:
"Unrecognised file type: open anyway?"
When I click yes, it opens it, and gives:
"File open error: can't find video or audio tracks."
So I think we can confirm that (1) the file is mutilated and (2) iTunes did this during the "writing tags" tagging process, which I terminated early. I would be interested to know what goes on within a movie file during tagging that could affect the main file content data in this way.

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#1. Why can’t my iPod play MP3 video files? And why do I have to convert to almost all the same settings except changing it from an mp4 to an m4v. according to Apples own site I should be able to play .m4v .mp4 and .mov files!! Note: remember iTunes plays them fine but my iPod will not.
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#3. Why is the conversion so slow? Please speed it, you have the power. Convenience is the thing that sells products.
#4. Files that cannot be played on the current iPod need to be easier recognized for simpler cleaning.
#5. Also make an easier way to select all dead link files for faster cleaning, deleting, etc. This one is important.
#6. Make a user friendly way to change where my files are going to end up once I convert them for iPod more options and better customizable settings are need.
#7. One of the most important is ADD A SEARCH OPTION. I and we classics will LOVE Apple for it.
For you readers, I apologize for the long post, and any grammatical errors you might find throughout it. These are problems that I have faced with these programs and hardware and I wanted to make sure they got acknowledged and hopefully addressed. Any information about why I cannot play MP4 Video files on my iPod would be the best. If anything in my post gets answered that’s the one I want most. Will save me a lot of hassle.
Thank you all and I look forward to your suggestions and comments. All are welcome and appreciated.
Sincerely,
Bond, James

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