I can confirm this behavior, but have no solution yet.
I am on Mint 12 (lisa) LXDE, using an apple keyboard.
Some things I thought while the problem occured:
1) that it only concerned the multimedia keys on my apple keyboard.
2) that it only concerned sound of my command line mplayer.
When watching movies using command line mplayer I would accidentally press mute instead of volume-down. I then had to unmute using the desktop taskbar(?) sound icon. After having to do this a number of times, mplayer muted permanently. But other movie players did still give sound.
I then tried to fix this, ... the wrong way,... and broke all sound on my system. (installed mplayer2, but that broke my 10bit video decoding, which i cannot live without..
, then tried to install ffmpeg > 0.7, without knowing what i was doing. After that the system never gave sound again... LOL ) Finally, reinstalled MintLXDE.
However, after reading your post I think it may be a more general problem than just the mplayer-apple-keyboard interaction.
I will get back if I do find a good solution. In the meantime I am a little afraid to experiment too much, as I broke my mplayer (and system) by doing so last week.
What I do now is use the normal "m" key to mute my mplayer, instead of using the multimedia mute button on the apple keyboard. Sofar, "m" has always unmuted for me...
Hope this helped a little,