This sounds like some sort of video driver or hardware issue, as it’s the first instance I’ve heard of it and it does not happen to me. Can you try updating the driver for your video adapter? For Nvidia, you can get the latest version from http://www.nvidia.com/Download/Find.aspx?lang=en-us . Just remember to select your video adapter series (600 if you have a 670, for example). For Intel and AMD, I’m not sure as I haven’t looked it up. Google will help you there.
If it still flickers like that with the latest video driver, it would be interesting to see your log. Put “retroarch.exe -v --menu > output.log 2>&1” in a batch (.bat) file and run it to generate an output.log file, then pastebin it here.