Freddie, why don't you try deleting the /etc/rc6.d/K50alsa-utils ? That script 
resets the volume settings, so if you remove it you preserve your mixer 
settings. The /etc/rcS.d/S50alsa-utils is not necessary.
It worked for me.
Distro: Xubuntu Jaunty x64

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[Jaunty] Sound card outputs start muted after recent updates to use pulseaudio
https://bugs.launchpad.net/bugs/315809
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