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I've been having some problems recently with the sound in Ubuntu Linux (Jaunty). One of the issues is that after each restart / boot-up, when I log-in to Gnome, the sound is muted even though it wasn't when I shut down the computer, so I searched for a fix (I've read it's a Gnome issue) and found one and I will share it with you, as there must be some other people having this problem with PulseAudio (i'm not sure if it's a PulseAudio problem though).

The first thing you need to do is set the sound to a level you want it to be saved and then restored. After that, run this in a terminal:
sudo alsactl store
The above command saves your sound level but does not restore it after restarting. To restore it, you need to run the following command:
sudo alsactl restore
To have your sound restored after each system restart, edit the /etc/rc.local file and paste the above command right above "exit 0":
gksu gedit /etc/rc.local
And add alsactl restore there.

Also, make it executable:
chmod +x /etc/rc.local