Yeah, I'm stumped too.. Funny thing is like I mentioned, it works fine when I set my primary display to my monitor but when I put it as my TV screen I get that flashing. Also, when I disable Crossfire it works.. which sucks.. I just tried deleting all AMD drivers in device manager and used AMD cleanup utility and reinstalled all drivers and still same issue. I even tried flashing one of my GPU's bios and still..
EDIT: I have an idea which I'll probably try tomorrow as it is late now. I have my TV hooked up to HDMI and my monitor is DVI. I think it may be my main GPU's output that might be causing the problem. I'm going to try to swap around the GPU's tomorrow and see how it fairs and if my hypothesis is correct.
2nd EDIT: wow.. so it is my primary GPU that's the issue. I took out the plugs while it was blinking and reinserted it and it swapped monitors, making the pc monitor flash while the tv worked albeit with a bit of discoloration.
damnit.. so without physically swapping GPU (PCIe slots) and just switching the display out ie. as in plugging the input into the 2nd gpu ports, the same thing happens.. not sure what the issue is and if me switching PCIe slots will even make a difference now.. back to sq 1.
3rd EDIT: WOW.. seems its a driver issue? Dragon Age Inquisition booted up in fullscreen and utilizing both GPUs without any hiccups. Earlier flashing problems were tested on Gone Home and Dragons Dogma. Which begs to question if these issues are because of non AMD optimization?