Este artigo wiki do Gentoo pode ser aplicado aqui: Controle de volume por aplicativo do PulseAudio :
PulseAudio supports per-application volume control, but by default this doesn't do much as you can only control these volumes from the pulseaudio volume control utility. Meaning that in an application like Audacious, when the output device is set to PulseAudio, and the volume control is set to hardware, it will adjust the master volume control, not the per-application volume control.
To fix this behavior, set the following in
/etc/pulse/daemon.conf
flat-volumes = no
Now whenever Audacious goes to adjust the volume, it will adjust the audacious only volume and thus you wont have multiple applications fighting over the master volume control.