I guess i have overlooked something in the guide that might help,
9.17 Fix for Ubuntu 8.04 (kept removing directories upon reboot)
Edit /etc/rc.local and add the following before the exit line:
chown -R postfix:www-data /var/run/MailScanner
chown -R postfix:www-data /var/lock/subsys/MailScanner
The reason I didn't even think to read this, is that its all strikethrough.