Does the server show up in the Server list as (Master)? If so, delete it, make absolutely sure your DNS set up and try again.
Even though I hsve a fully qualified Domain name, SERVER.DOMAIN.COM and my reverse lookup set weith my ISP. if I do a lookup for the IP of my server it returns server.domain.com, found Open Directory was much happier if I used the DNS server on the Server Itselfl
In Server DNS created a Primary Zone for my doman, domain.com. Then a Machine A Record for server,domain.com. It automatically made a nameserer record of server.domain.com and the Reverse Zone and server mapping for reverse lookup. Then set it to perform lookups for this server only. Then set 127.0.0.1 as the First DNS server in System Network Settings before any ISP DNS Servers. Then for good measure also entered my ISPs DNS servers in as forwarding servers. Then setup Open Directory with the correct domain with no errors.