I read in a post here a long time ago, around July, abut Samsung LCD HDMI and Apple TVs. I have a Samsung Plasma and while watching a movie (either on ATV or my Samsung upconvert DVD player) the screen will flicker and the audio will go out for a split second and return to normal. I contacted Samsung about my issue and they blew me off saying to upgrade the firmware, it is up to date, and then they said unplug all the cables and count to 30 (stand on one foot singing twinkle twinkle little star 😉 ) at which point I considered myself blown off.
Anyway I cant remember what model Samsung LCD this person had, but it was one of the newest ones at the time, he said that Samsung told him that they do not support Apple products... and there was some more along with it but it sounded like they were reall A-holes about it.
Like Winston said, your best option is live with it and hope some kind of update resolves the issue to some extent. If there is new firmware available for your Samsung, all you have to do is download it from their site (you have to register your TV and all that with the serial number... and stand on one foot 🙂 ) and dump the files on a USB drive and plug it in to the TV and initiate firmware upgrade from the TV menu (at least thats how its done on my samsung plasma...). Unfortunately for me there is no new firmware, no light at the end of the tunnell. I just thought you might like to know that other Samsung customers are suffering from their lack of HDMI support. My father in law has a Samsung plasma and for the longest time it wouldn't work with his Dish Network HD receiver. Oh and my Samsung plasma is slow to detect the Apple TV's HDMI signal. I'm tempted to go get premium cables one day to see if that makes a difference on either issue. Supposedly from what I've glanced at round the net there can be quality issues with the cheapies like I got at Wal-mart (for only $19.99, what a price! Thanks China!!!) so I'm now bothered by that thought every time it glitches (maybe once or twice an hour).
Good luck with your issue. Check that firmware for your tv and if you feel like trying, try calling Samsung and see what they have to say. Who knows, you might win the samsung support lottery!!!