I have this same issue. I was running an experimental build of VMWare Fusion 8, and I had this problem. I assumed it was a problem with the test version, and I finally paid to upgrade to the real v8.0.2. The problem still exists.
I affectionately call it "epileptic mode," but I'm rather annoyed that I paid now and it's still an issue.
What I've noticed is that, if an OS X window receives an update on my main display while I am using Windows full screen on another display, the updated OS X app will go crazy. It's as if it toggles between the new update and the old view prior to the update. Does that make sense?
For example, if iMessage was open, and I received a message from someone while working in Windows, it'll quickly flicker between the view before the message arrived and the new view with a new message.
It's like the double-buffering is going crazy.