The following ports are open (I guess from when I first installed fm server):
fmsased, fmserverd, fmserver_helperd, fmsib, java, python, scsd.
Ports are identified by a number and FileMaker Server documentation specifies specific ports that must be open. I would guess that one or more of these is not open now the the firewall is up.
I saw those ports in the troubleshooting. However, I'm on a Mac, which doesn't use port numbers in the firewall. It uses program names.
I have only done this for windows systems so that may be the difference, but the documentation I've seen on my windows system requires that multiple ports have to be open and each was designated by a number.