Using xfce 4.8 on Xubuntu 12.04 with pulseaudio removed.
xfce4-volumed relies on xfconf's property xfce4-mixer/active-track for name of master channel. So, if you change master channel via xfce4-mixer-plugin, xfce4-volumed would still use old value (by default this property does not exist). That is, xfce4-mixer-panel would change volume for one channel, and media keyboard buttons - for the other.
Quite straightforward fix would be to update xfce4-mixer/active-track (and create it if it does not exist).
Another thing that would be nice if xfce4-mixer-plugin would store master channel name only in one place, in the same as xfce4-volumed does.
This is really up to xfce4-volumed, please open a report at https://launchpad.net/xfce4-volumed Note that since version 4.9.0 the panel plugin stores its configuration via xfconf and it can also optionally handle keyboard shortcuts.