Working with Quicktime files on your timeline.

I'm working on a project where I'm using clips from previously created videos that are in Quicktime format. I'm also using some footage straight from my DV tapes. When I go to export this project, many of the clips are off. They'll be of slightly different footage (right before or after the desired clip), the timing will be off, transitions are in slightly different places, etc. The clips straight from DV are preserved, but the other ones come out all wrong when I export it to DVD Studio Pro or as a Quicktime file.
(I also put those clips from previous Quicktime movies on my timeline and then the next time I go to view them on my timeline, they're of a different scene and do not play the way I left them.)
I have been using Final Cut Pro and other editing softwares like it for many years now and have never come across something like this. Does anyone have any insight into why clips from previously created videos are not preserved in my new project and the movie I export comes out with the clips/timing all out of sorts.
I appreciate any help!

BlurredLens wrote:
I'm working on a project where I'm using clips from previously created videos that are in Quicktime format.
'Quicktime' or the '.mov' extension isn't a format, it's a wrapper, ie- a brandname that is stamped on anything 'made' by/for quicktime.
To find out the true format of these problematic clips, open them in QT and press cmd+i to get basic info, or in FCP, select a clip in the browser or timeline and press cmd+9 to view item properties... here you will actually see the true format.

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Hello,
My team and I have been following this thread - we've been having very similar issues. Namely the 86::2 error and "MooV file is damaged or unsupported."
We had these issues on two machines from the first time we ran Ae CC and Pr CC early last week and were on OS 10.7.5. So we did a clean install and upgraged to Mountain Lion.
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Adobe Crash Report Links:
https://dl.dropboxusercontent.com/u/8857265/Adobe%20Troubleshooting%20-%20Reports/Adobe%20 QT32%20Server_2013-07-31-150909_Edit-TWO.crash
https://dl.dropboxusercontent.com/u/8857265/Adobe%20Troubleshooting%20-%20Reports/After%20 Effects_2013-07-31-154601_Edit-TWO.crash
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