I know this is old, but I've been consistently trying to find an answer to this same problem. I have the same HT system, with DTV and XBOX 360 hooked up through the HTS to the TV. When playing a game, or watching a video or doing anything that has nothing to do with the DTV, I don't have any problems. However, in most every show, particularly in darker scenes, I get flickering, or flashing on/off really quickly. Sometimes it happens 3 or 4 times rapidly in succession, some times it happens every 10-15 seconds, and sometimes I can watch a whole show without it doing it. I have switched out HDMI cables for things that are working properly with the DTV box, and have tried it on three different DTV boxes, but still have the same problem.
Did you ever find a resolution?
I got the HT-D6730W a couple weeks ago, and it's my first HTS. My setup up until getting the system was a 60" LG plasma, with cable box and PS3 hooked directly to it via HDMI cords. No troubles.