I also have setup the external player to be used with mkv and mpc. With some mkv files mpc will opened but mostly it doesn't. When mpc opens MC stays in front. The MC screen should be minimized when MPC opens en return back when you stop the movie.
Was this ever resolved? I am trying out MPC-HC as a player because my BD rips of TV series to MKV won't play back smoothly in the VMC player (stutters and audio gets off). MPC-HC seems to be able to play them well but I can't get it to play nice with MB. Having all the problems reported here - MPC opens but behind the MC window, etc.