I'm sorry to hear that you're having this issue.
Try changing the output resolution in the HT's menu to see if changing it to a different resolution eliminates the flicker.
You might also try swapping out the HDMI cable to see if that's the cause of the issue.
I can't find a resolution to this problem anywhere on the forum, so if this is a repeat, I apologize. I have a brand new Samsung Series 5 LCD TV and Samsung HT-C5500 home theater system hooked together. Whenever I play any type of BD, DVD, the screen flickers.