Hi,
we have a similar problem in having exports to ProRes422 that are off by a frame (out of sync). In our case the very first frame is duplicated.
This we experience on sd as well as hd projects and most our projects are edited with native .mxf files but .mov files have produced the same problem sometimes.
We have not been able to pin this down to a particular format or workflow and keep searching.
I will experiment with having a title run along the whole sequence to see if the problem goes away.
And I will come back to you if we make any progress, just in case it helps you too.
Patrice Freymond
Editor  Certified Trainer FCP7/X
Post Consultant
Always learning…