Quicktime won't play HDV .mov

I upgraded to Lion, and noticed that Final Cut Pro was not playing my HDV .mov clips off of an external drive in the timeline.
Upon closer inspection, Quicktime also couldn't play these HDV clips either. Quicktime X said "The document ... could not be opened. This media may be damaged." Quicktime Player 7 (Pro) says "The movie could not be opened. An invalid public movie atom was found in the movie."
I then take this same external drive to a Snow Leopard installation, with FCP on it, and all clips work fine, and can be opened in both Quicktime X and Quicktime Player 7 (Pro).
I can also open these files in VLC in Lion without an issue, so it seems that maybe it's a Quicktime codec issue. I look in /Library/Quicktime/ and the AppleHDVCodec.component is there.

Thanks for your help with this, it is very kind of you.
As I understand it, a flattened Quicktime file is one where all of the information of the video and audio are interleaved in the data track. In a non-flattened file, this same data can be spread across a resource fork and a data fork, and can cause issues with certain applications. The files my Direct to Edit (DTE) machine makes are not flat. I think I can make my DTE create a different filetype of footage that'll work properly in Lion and FCPX, but my hours and hours of existing footage that is not flat will have issues.
Before OS X, I remember having issues sharing Quicktime files with Windows users; even if they were using Quicktime. The simple fix was always to flatten the file (usually just opening the file in Quicktime and then re-saving the same file--not re-encoding the file to a different codec or anything, just re-saving it), and the file would then be flattened and work in Windows. I've never had any issues with non-flattened Quicktime files in OS X until I downloaded FCPX on a Snow Leopard machine to test it out. I tried to import the media that works just fine in Quicktime and FCP7 into FCPX and it said it was an unsupported media file. Flattening that same file made it work just fine in FCPX.
It appears to have the same result in Lion--Quicktime suddenly can't read non-flattened files. I wonder if another good test of this would be to use iTunes in Lion. Usually, if you have a movie file in iTunes and add metadata or change metadata through iTunes on that file, the file is not flat. I wonder if Lion would then not be able to be read it?

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