Thanks colin. I had suspected the avwizard was modifying the asound.conf file. Is there any way i could find what the trigger is at all? Or an easy way to restart alsa sound whilst the system is up and running to see if that helps?
I have found the wiki relating to preventing the modification of xorg.conf but it doesnt really give much in the way of clues for sound;http://wiki.linuxmce.org/index.php/Custom_Display_Resolutions
Prevent LinuxMCE from changing the Xorg config
This is a bit of an ugly hack, and if the above is done correctly I'm not sure if it's even needed. Nevertheless, if you want to get really creative and write your own xorg.conf, this is the way to protect it from being overwritten:
Edit /usr/pluto/bin/Xconfigure.sh and add the following lines immediately below the #!/bin/bash:
echo "$0 neutered to preserve custom xorg.conf"