I bet the change of volume level in mplayer is also changing the system
wide volume. It happens because you are not using software mixing. To
enable it in GUI version of mplayer (gmplayer) go to Preferences/Audio
and tick "Enable Software Mixer" option.

If you use the no gui version you need to modify ./mplayer/config file. Add the 
line:
softvol = "yes"

-- 
muting sound in mplayer causes rhythmbox to mute
https://bugs.launchpad.net/bugs/107751
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