Video "pops" after quicktime export

exported my sequence (apple pro res 422 1280x720 59.94) as a straight quicktime movie export using current settings and make movie self contained. when i play the quicktime, there are "pops" - the picture jumps either forward at a fade up from black or jumps back at a fade down to black. the "pop" happens right at the end of the transition if there's fade up or the first frame of the transition if it's a fade done. the fades are to & from slug (black). it's as simple as it could be. also when lower third titles fade up & down on track two the same thing happens. i've rendered everything which i thought was overkill. i'm going to try exporting using compressor next. i've never seen this happen before. any ideas? thanks.

michael, the orig clips are pro res with exactly the same settings as the sequence setings.
using compressor as opposed to using make quicktime movie did make the sequence without the "pops" or jumps that i was getting using make quicktime movie though it took twice as long. since i have a bunch of these to do and they're 2-2 1/2 hrs long would prefer to use qt as opposd to compressor.
if anyone has any ideas i'd appreciate it. like i said as soon as the fade up from blk/slug ends, the picture jumps forward. conversely at the exact frame the fade out begins the picture jumps back. however when the quicktime of the sequence is reimported and played back in fcp, the jumps are not there. wondering if there is prob at all but obviously "something" is funky otherwise qt player wouldn't being having difficulty playing the clips. thanks.                                                                                             

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