If your desktop background has been set to change periodically then turn it off. It seems, for me at least, that when ever time something changed on the desktop e.g the wallpaper or a icon in the system tray, it would render over the top of the game resulting in flicker.
I've been having the same flickering issue, and it seems like when my background changes to a new image is when it does it each time in the game.
I'll disable that and see if it works!
After I disabled my background shuffle it's a lot better, but it does seem like anytime there's any sort of activity on my desktop it flickers for that, too.