Comment 6 for bug 403609

I have a similar problem (if not the same). I figured out that keyboard shortcuts operate on "Master Volume" instead gnome-volume-applet let you choose the channel to track. In my case, the channel "Master" doesn't affect the output volume at all. The real master volume is instead "Headphone". This is a common problem due to non perfect sound card detection at kernel-level, and explains the channel chooser option in gnome-volume-applet.

For desktop consistency, you should force keyboard shortcuts to operate on the channel chosen in gnome-volume-applet.