I have Fedora 20 + VLC 2.1.4. Whenever I change the volume in VLC, it affects the volume of my system as well.
Is there some setting/config that I can modify to prevent this from happening?
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This is due to
As mentioned here http://wiki.gentoo.org/wiki/User:Feystorm#PulseAudio_per-application_volume_control
PulseAudio supports per-application volume control, but by default this doesnt 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.
So, to fix this behavior set
flat-volumes = no in
/etc/pulse/daemon.conf to enable per-application volume control.