I think I recall running into this when the apple update service was running after an extended time of being turned off. If I recall, I just let the computer run for half an hour and rebooted. That was years ago (FM10 era) so I'm not sure if it's still an issue.
What I do know is that by default I turn off the auto-start of filemaker on servers now, the manual control has never given me problems, and offer me opportunity to take care of necessary system work before booting up filemaker.
Thanks, but I'm not sure that was the issue. The issue was that the admin server wasn't running, so I couldn't access either the command line or the Web based admin tools. Fortunatly a couple of reboots resolved it and I was able to login and get things going.