I'm just incredibly busy at the moment and usually only reply after I've had a chance to look into something in detail. In your case, I'll need to create a version of Remote Buddy with debug output and run some tests.

What I can already tell you now, however, is that both "Mute" and "Play/Pause" are mapped to the Select and Play/Pause buttons of the aluminum Apple Remote by default and that - unless you have changed that default mapping - these actions are the expected reactions to presses of these buttons. Right now, there is no code that ignores button presses that were used for waking up the computer, because the reason due to which a computer wakes up is not easily detectable.

I hope to find the time for a debug version and tests in the course of the coming week and then get back to you with the results.

Thanks for your patience.

Best regards, 
Felix Schwarz