Thanks Till, turning on debug logging didn't log more than what was already in /var/log/messages as far as I can tell.
The interesting thing is that when I ran the server.sh script manually BIND config files were updated, however after re enabling the script as a cron job again config files are not updated.
I didn't see any errors in manual run of server.sh.
I run many servers running ispconfig and I have never run into this situation.
Any further advice would be greatly appreciated.