I'm running Windows 8, or 8.1 (the computer was talking about forcing me to change to 8.1, so that may have already happened). The only flickering issue that I have experienced is on the mission briefing screens. The planet flickers horribly, but in game there is nothing like that. I will say the screens flicker SORT OF for me, but not nearly as much as you describe, it is only occasional and just makes them be sort of choppy.
Have you tried different screen resolutions? Mine is set to 1280x1024 or something like that.
My video card is ATI though.