I have the problem with with Mute and VolumeDown keys in Ubuntu 14.04 on my Thinkpad X61. These two keys just stopped working after relogin.
I tried to run
gsettings reset-recursively org.gnome.settings-daemon.plugins.media-keys for my user, but this did nothing.
Keys are hardware OK (I can see them pressed by
xev and also can use them as hotkeys in Audacious, also they work correctly for the Guest session). But system wide I can raise but not lower volume using keys. In Settings > Keyboard > Shortcuts Ubuntu can delete and set up these keys again, so the system does see them. They just do nothing for some reason.