Remote Buddy makes no difference with detecting apps - no matter how 
they are started. So I guess, you have two copies of MPlayer lying 
around (maybe one in a backup).

When you start Mplayer through MythFrontend, right click on Mplayer's 
icon in the dock, then select "Show in Finder" to see where that 
application is located - whether it's the same version, a copy or 
whether it's just a part of Mplayer that gets started can then be 
easily determined.

Best regards, 
Felix