Bad Public Atom in .mov  file

I upgrade to Quicktime Pro in order to export my .mov movies taking from a Nikkon Camera. I can play the movies but when I tried to export or save for .flv format, I received this message:
"error -2002 Bad Public Atom in the movie file"
Please I need some ideas or solutions about this issue. I check in the internet and is too many people having similar problems.
Thanks

Many of the newest movie trailers hosted at Apple are encoded using the new H.264 video codec.
You should be receiving a "component not found" message because your version of QuickTime can't display the video portion of these files. The "bad public atom" message should only appear if the data structure of the .mov file has been corrupted.

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