Comment 26 for bug 449783

Adjusting the volumes separately is pretty much the defining feature of pulseaudio. The gnome volume applet is probably just for controlling alsa. I use Xubuntu, so I don't know if this will work for you, but if you right-click on your volume control icon from your panel, there should be a Properties or Settings or something to click on. You can change the command to pavucontrol, so that may be more convenient for you.