I have the PCM controller that cannot be set to mute. The mixer doesn't handle such controllers, in fact it provides the mute button while it should be greyed out. I have recorded a video to understand what happens: http://mykey57.free.fr/pub/tmp/mixer.ogv In text, when I mute the controller, it passes in reality the volume to 0. Then the scales have no effect if they are moved, unless I uncheck the mute button. I hope there is something in gstreamer for that…
I can now reproduce it here, so I'll have a look at it later today.
It seems to be a GStreamer issue. I've filed a bug against gst-plugins-base on http://bugzilla.gnome.org/show_bug.cgi?id=555248.
There's no way to fix this in the mixer. Bug against GStreamer is filed so I'm closing this one.