OK fixed.
I noticed in the server settings section the zone path dir was somehow set to /etc/bind which doesn't exist. That explains the missing zone files.
I set it to /var/named/chroot/var/named/ and saved it then made a change to the DNS and it recorded the entry.. yippie
server_bind_zonefile_dir in the config DB now shows /var/named/chroot/var/named/ and works fine now
