I recently bought the Hobbit 3D and noticed the same thing.
I tried every setting on my player, amp and TV, but nothing worked. I'm glad I'm not the only one experiencing this.
My setup is as follows:
Yamaha BD-S673 player
Yamaha RX-V671 receiver
I noticed that static images, like the background, seems to be perfectly in place and crosstalk free (most of the time), but fast moving objects, like actors' hands, seems to be jumping forwards and backwards in depth. I also noticed a lot of crosstalk in places, as if the frames were out of sync (like you said).
I hope someone finds a solution to this. I would hate to buy another Blu-ray player .. again :-(