So -- right up front -- I'm running FMS 16 on a Mac 10.12.6 box *with Server.app* installed. This does function if you (A) remove Server.app, (B) install FMS 16 pushing the web ports to a different port (10080/10443) and then (C) reinstall Server.app -- I was instructed to this installation method by FM Support when FMS 16 came out and it works (including rebooting the server, etc...)
That said -- installing the new security update for 10.12.6 that came out this week stopped the ability of the FMS web server to be active (the console for FMS says "web publishing" is on, but the web server is not.)
I have a temporary workaround (which is awful) in that I can do the following:
1) Uninstall FMS 16.0.3 and reboot the server.
2) Remove Server.app and install FMS 16.0.2 (must use the older version)
3) Reinstall Server.app. At this point the FMS web server is operational.
4) Reboot server -- FMS web server stops working
5) Install FMS 16.0.3 *update* -- FMS web server starts working again.
But then I can't reboot my server -- or the FMS web server stops again. If I reboot the server, then I have to run through steps 1-5 again.
This only started happening after the new 10.12.6 security update (which, according to Apple support "does install a later revision of the apache server").
I had tried the security update on my trial FMS server -- but it's an older, slower iMac with a mechanical drive -- and had no issues, but my prod FMS is a much faster mini with an SSD, so this sounds like a race condition issue.
As I led off -- yes, I'm running "Server.app" and it's not officially supported by FileMaker. But there's a problem.