I have the same model tv and i have the same problem. I have been trying to figure out fixes but so far have had no success.
I just bought a Samsung LED LCD TV (UN46C6500), and it's great except for one issue. When playing movies in anamorphic widescreen (bars on top and bottom), the screen flashes a horizontal green line across the bottom of the screen randomly and annoyingly (often during quick camera panning). It's not an issue with cables, as I play them from a USB flash drive I plug into the back of the screen. Is anybody else experiencing a similar issue with Samsung LEDs?