I don't know if this helps any, but I have a copy of the movie Prometheus that is a 1080p M4V file, and there's a scene in the movie where the android is watching someone's dreamscape. The dreamscape is intentionally pixellated (it was in the original theatrical movie too) and that specific scene consistently causes skipping with my Samsung BD58. The rest of the movie before and after work just fine. The movie is played natively by the player (shows as MPEG in the menu), and doesn't do any transcoding.

I didn't have this movie prior to last week, so I don't know if it would have caused skipping in the previous versions, but I figured that it might help you to have more info.