Here's something, might be a bug, might be Matt trying to enforce discipline. This is NOT a version-specific bug--I've seen it for quite a while.
When I have two zones playing video simultaneously, say with dual split views, and in any combination of madvr or evr, if I send BOTH displays to my external monitor as full screen (so that only one is visible), and then raise a window above the MC program window (MC loses focus), the the two playback windows begin to exchange visible dominance. This will continue until the MC program window is restored to focus and the pulsing immediately stops and the original upper display continues.
Why would I have on full screen covering another? I often have multiple simultaneous playbacks. While I might have a movie playing on the external screen, my short attention span often requires me to have ski videos playing on the dual split program views. But if I see something I really like on the ski vid and/or the movie is boring, I'll double-click on the ski vid to send it to the external display and on top of the currently playing movie. Actually that much is fine, it's only when I then raise some other program window above MC (my attention drifting again) that the pulsing starts. Yikes!