I have a similar problem. When using my 480 over 60hz and I go into a game, my screen will blink on and off as well at the start screen. Mostly staying off. At 60hz the game works as intended. I have tried using CRU, updating the firmware on my monitor, this is my second 480 and the problem existed on the first 480 and the 2nd on I got after RMAing the first 480. When using DVI cable I can get the game to run at 80hz. With the Display Port 1.2 Cable it fails at 90hz. Haven't tried 90hz with the DP cable. The problem did not happen with my GTX 780 with my PX277 PIXIO monitor. I am finding mroe people in the community with similar problems. It appears to be a driver issue AMD has not fixed yet. I have literally tried everything I can think of, and when I post my problem on help sites like these, all the suggestions are things I have already done.
I have done more testing. Using CRU I am able to go as high as 71hz without the glitch. at 72hz the glitch appears where the screen will blink on and off in any game.