I too am experiencing this problem with my Apple TV 2nd Gen, both with content from the Apple store and downloaded content.
I have tried both wirelessly and wired from my MacBook Pro to my router, and from my router to my Apple TV. I have tried resetting it, restoring it, stopped it sending Apple information, streaming different quality video, all with no success.
I am streaming to a Samsung LE40A557 1080 LCD, and the only thing that made it slightly better, but still didn't completely resolve the problem, was changing an Entertainment setting in the TV to Game.
I am going to complete the feedback form to Apple and hope that this is a firmware issue and that they bring a fix in for it.
http://www.apple.com/feedback/appletv.html
Help Apple, please!