I couldn't reproduce the issue. I just fell into more confusion. I'm guessing you already killed pulseaudio, deleted the volume preferences from .config/pulse/*volumes* and restarted pulseaudio to see what happens?
On a freshly installed Fedora 23, I saw some fishy mixer behavior. Play a video on YouTube, reduce the volume using the main volume GUI in GNOME3, then start Rhythmbox, play some audio, adjust the audio to 100% there and you will see the master mixer go up to 100% as well. But if you go back to YouTube, the master channel will still be at 100%, but Firefox will be much too low volume to hear anything. The master channel has not adjusted Firefox's volume.
Yet when you go to "Sound" and adjust the Firefox volume back up to 100%. The next time you use the main volume slider, both the master volume and each individual volume of all audio streams currently playing, but not of streams not playing, is adjusted by the difference of the volumes. So if you had master at 25%, Firefox at 25% and Rhythmbox at 50%, then move master to 100%, you'll end up with Rhythmbox at 125%. Yet system-level notifications like the system bell in the Terminal would automatically now play at 100%. So already with just GNOME and nothing else, there is confusion.
Edit: The actual percentages are different. It seems to add a percentage to all mixers, they don't scale like I described, but it's still easy to push some application above 100% this way by moving the master channel in the mixer.
I'll try to find out what is breaking what here.
Last edited by Psy-Q; 06-13-2016 at 05:04 AM.
Reason: Made sequence of killing and starting pulseaudio more explicit
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