I wouldn't think that you'd have to change any conf defaults to start, is dnsmasq running already?
Try netstat -tulpn again to see if dnsmasq is listening on a port. If it is, use $ sudo /etc/init.d/dnsmasq stop to stop it. If that fails you can use $ sudo kill -9 to kill the process (same as lighttpd) previously. From there try to start piratebox again.
Try netstat -tulpn again to see if dnsmasq is listening on a port. If it is, use $ sudo /etc/init.d/dnsmasq stop to stop it. If that fails you can use $ sudo kill -9 to kill the process (same as lighttpd) previously. From there try to start piratebox again.