It is inherent to the operation of OS X Server to change the hostname at startup, but you can stop your server from informing you about the error by unchecking Network configuration change in the Delivery tab of the Alerts section in the Server app.
Happens on my server, used to happen all the time. Now, only when I establish a VPN connection to the server. Just applied the new updates, no change. I have reverse lookup configured with my ISP and a static IP. The server is behind a firewall.