Just got a new MacBook Pro with Retina display and had a heart attack when 3 days in the display started flashing blue and yellow, almost like a refresh problem. After resetting the NVRAM (which had no effect on my issue), clearing out bad color profiles, deleting caches, etc, I was ready to head to the Mac store. Luckily, I tried one last thing which was to disable Automatic Graphics Switching under the Energy Saver system preference.
Once this was disabled I haven't seen the problem since. Hope this helps someone else! I imagine this happened after an update was applied, but I have no proof of that.