While I'm sure there are plenty of knowledgable people here at ATOT on this matter, I'd recommend posting this over at
the Audio Video Science Forum.
I have an account there and as far as Home Theater 'Geekness' goes, you'll find no better site on the Internet... Period!
I'll bet they can answer your question spot on and in fact I'll bet dollars to doughnuts that the issue has already been raised there several times and a quick search may be all you'll need to get to the bottom of your problem.
I noticed the same thing on my projector when setting my DVD player to progressive scan mode. It seems like the PJ was performing it's own upscaling on and already upscaled image from the DVD player and somehow the sync was getting off a bit. Or something like that

.. At any rate the bottom like was sync issues between my DVD player and my projector...
My solution was to replace the DVD player YMMV.
JR..