Try turning the AutoMotion Plus setting to OFF or a different setting to see if that improves the symptom you're describing. When you say skip, do you mean the picture itself seems to skip, or the screen goes black?
I recently purchased a Samsung UE55C6540SK 55" LED TV, aswell as the Samsung HT-C5530 blu-ray home cinema system. I have it connected to a SkyHD+ Box and an XBOX360.
The problem is when I watch Blu-rays and very infrequently Sky HD Channels, the picture will sometimes jerk/jump/skip much more frequently on Blu-rays (every few minutes on Blu-Rays - Its happened a lot on every blu-ray I have watched). The television software is up-to-date and I have updated the Blu-ray firmware. I have checked all the connections and I am using Monster Cables which I was told in the shop I purchased it from were the best kind.
Thanks in advance