So when you import the aaf into AE it takes the .mxf avid media files and makes it's own copy that has a .mov extension. Am I understanding this correctly? I would take that to mean AE is rewrapping the video essence into a QT wrapper and not just changing the extension. Again I'm only speculating out loud. From what you say it sounds like the time code is getting changed in the process. This points to the possibility that there may be something going on with the pointers from avid and whether they are getting changed because the aaf is using consolidated media as it's reference as opposed to the original full length clip. Maybe something like that is counting just the handles from the first frame of the clip instead of referencing actual time code. Like when you decompose an imported clip with handles and then a subsequent batch import only counts the handle length from the first frame of the clip which can lead to all kinds of shifts or fits to fill etc...
When you say the time code is off is it close but off are completely in another world hours away?
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