I'm also affected by this issue, also in Jaunty (x64). Once I'd unmuted the sound controls using gnome-volume-properties, 'sudo alsactl store' didn't work for me; I had to change the permissions on '/var/lib/alsa/asound.state' first (to 0777) before running the 'alsactl store' command as myself, then change the perms back to 0744 when done.
I'm also affected by this issue, also in Jaunty (x64). Once I'd unmuted the sound controls using gnome-volume- properties, 'sudo alsactl store' didn't work for me; I had to change the permissions on '/var/lib/ alsa/asound. state' first (to 0777) before running the 'alsactl store' command as myself, then change the perms back to 0744 when done.