I have the same problem. I have a new MBP with a thunderbolt port, which is connected to an Apple 24" cinema display, using the new thunderbolt port. I am experiencing one second black outs every few minutes, and fairly regular jitters once the computer starts warming up and crunching some numbers. The shift never occurs on the 15" monitor, only the external. I also still have my old MBP with a mini-display port, and the external monitor works perfect with it.
I've had a case open with Apple since getting the new model last month. Apple has actually been very good to me, and I'm not too worried about the issue long term, as they have acknowledged the problem to me and have not once tried to shift blame. They even swapped out the new MBP the next day, thinking it was an isolated issue. It wasn't, and it did the same thing on the second version. They then put me in contact with their engineering department, as they said I was the first to report the problem. I submitted several videos of the issue, both of the 1 second blackouts and the numerous external display jitters (quick digital shifts of the screen image). I also reinstalled the system software clean, so I had no 3rd party software on the computer and then downloaded their technician "capture data" application, which a user can use to time stamp an issue, and it records all of the behind the scenes data for Apple to analyze. I sent them numerous captures.
It sounds like it is now a known issue, but they are trying to find a firmware fix, as that is obviously their best and cheapest option. I'll post again when I get new news.