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Premiere or AME dropping frames in clips in sequence like a time remapping

Update:10-11Source: network consolidation
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Very strange issue. I have had it happen twice now with two different projects.
I have a timeline setup as 1080 using the raw MOV files from a Canon 60D. Everything looks good. I then render the media and with the output file, one of the clips looks like it is running at an extremely low frame rate. Maybe 1 frame a second almost. but it does not do this in Premiere. And this is why I think it might be with Premiere and not AME....
I found the file I got the clip form and selected a new segment of video to use as my clip. I inserted it into the timeline just before the one that was giving the frame rate issue. I then removed the clip that had the bad frame rate issue (again, only after it was rendered in AME can you see it in the rendered file..it doesn't do ths within Premiere playing the timeline). I then rendered the project again. This time, the clip I replaced looks fine, but the one right AFTER it now has the same frame drop problem. I have no idea what could be causing this. Neither of the clips have any time ramping. Neither does this in Premiere when I play the timeline. It only shows up in the final file I render, but moves down the timeline to the next clip when I fix the one that did it.
Any ideas on what is causing this? Anyone else ever see this?
Thanks.

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Jeff
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