Thank you for your post!
To my understanding it should be updating to fmp://FQDNfromCert/FileName as you Group Launch Center did. Have you restarted the Server since setting all of the Group Launch Center stuff up? If not, I'd recommend starting with the restart. It may update these links for you.
In the mean-time I'll look into other possibilities.
When server was first installed, I imported the settings from the old server, installed the certificate, and Restarted the Windows Service. The server has been restarted a number of times since then, most recently in May.