I've just checked with RC1 of Mplayer and could reproduce the problem.

Mplayer now launches Intel and PPC specific sub applications with 
invalid bundle identifier (all being just four questionaires "????"). 
These sub applications will accept keystrokes to be used just like 
previous versions, but they are not identifyable by bundle identifier 
anymore, so they can't be easily addressed. The main window will - 
unlike in previous versions - not accept any keystrokes anymore. 
That's also why we're seeing that problem.

Mplayer has been very inconsistent from a remote control view across 
versions, builds provided by third parties and the original dev team 
alike, with RC1 being the biggest challenge to date (yet not 
impossible to deal with). I've added the issue to the todo list and 
will eventually rewrite the Mplayer plugin.

Until then, please use an older version that supports control via 
keyboard through its main window.

Best regards, 
Felix