I've got the same problem with my new 2.3Ghz i7 mac mini. Actually it's quite consistent: when I turn on the mini in the morning, I can be sure to see one single flicker within the first minutes while it's running. And then maybe one more somewhen during the day. My monitor is an HP LP2475w, connected via HDMI-to-DVI adapter that came with the mini.
Another thing I've observed is that when the screen wakes from standby mode, it comes up, just to go black for a split second again before it stays on. With my old 2010 mini, the screen came back and stayed.
Yet another maybe graphics-related issue: when I use screen sharing to access the new mini, it can happen that I only get a dark gray screen on the first attempt. On the second attempt, I see the remote desktop.
Annoying, yes. I've pretty much decided to keep my mini nevertheless though, because I don't expect that I get one that works better if I go for a replacement now, and I don't want to go for an iMac or even a PC. And I am confident that the issue will get fixed eventually, either through a software update or an exchange.