Just a shot in the dark. I'd run into this in Gnome maybe as
far back as slackware 10.0 & also when I'd first booted ubuntu.
With slack, I'd have the volume all the way up, & nothing. Then,
I'd open xmms, & I'd find the volume there was all the way down.
Turning it up in xmms did the trick -- all sound worked fine.

I might have been able to find another solution in ubuntu, but
after a few days without sound, I'd downloaded & installed xmms,
found the volume down again, turned it up, & all sound
(naturally) was working.

I have no idea why system sound was turned down till after
installing xmms, it may be a Gnome issue.

Check Rhythmbox & anything else which plays music that you have
installed. If worse comes to worst, installing xmms isn't a bad
thing & will likely fix the problem.