You can try re-running the filemaker server deployment wizard. Chances are the OS upgrade disabled something used by the web publishing engine as part of it's security protocols. Running the deployment wizard or reinstalling filemaker server would correct these settings.
Make sure to save your filemaker server config to a file and backup your files before starting.
As a quick check, you could also run the following commands in terminal to restart the filemaker server and WPE services to see if it's that simple:
fmsadmin restart server
fmsadmin restart wpe
Since those would have restarted anyways after a reboot of OSX, I don't think they would work, but it's easy enough that it's worth a try. (note the first command will require the server admin console login user/password, and will also boot anyone that's connected to a database).
Thanks for your thoughts on this, Mike - really appreciate it.
I'll pass these suggestions on and see what comes of them.