In my experience using the QE, if my Flash doc frame rate is anything other than 29.97fps, I will always experience dropped frames and/or some frames where the content is visually affected (noticeable slicing and general destruction and interference of the image). If I change to a 29.97 frame rate and export again, the MOV is frame accurate and all images in all frames look perfect. But this may be getting off topic from the original issue. I would also try copying all frames and actionscript to a new CS6 document and try exporting again.
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