I don't run SMB. But most of the init scripts need to be run as root. So if you have some GUI interface you're using as a non-root user, then it either uses some setuid program to run the init script, or it uses sudo to run the script...
But really, I'd expect Samba to start a boot -- it's probably just a matter of dropping to a shell and doing a "sudo /etc/init.d/smb start". And perhaps figuring out why smb didn't start on your last boot.