Remote Buddy's menu is just a regular window, which by itself can't flicker.

Some applications write directly into the frame buffer memory of the graphics card when running in full screen mode to increase performance. If they do so without locking the screen for exclusive access first, they'll inevitably run into conflict with the regular OS X windowing system - which otherwise manages the frame buffer's content and which is responsible for compositing all window's content into it. You'll only notice this conflict when another window is to be displayed on top of the full screen window of the application writing directly into the frame buffer without locking - which seems to be what's happening here given your problem description.

The fix in this case would be for Plex to obtain a lock on the screen before writing directly to its frame buffer, thus avoiding conflicts with the regular OS X windowing system. That's what f.ex. Front Row and Keynote do. There's nothing Remote Buddy can do about it or that can be done by Remote Buddy about it.

Best regards, 
Felix Schwarz