Same problem here.
I just updated FM Server from 12.0.1 to 12.0.3 (OS: 10.6.8) and at the same time I ran software update which included "Java For Mac OS X 10.6 Update 16" which I think is what caused the problem.
On restart the only processes owned by fmserver in Activity Monitor are fmserver_helperd and fmserverd. EDIT: there are actually 5 more processes owned by fmserver (I thought typing fmserver in search box would show them but no). They are fmsased, fmsib, fmscwpc, FM Web Publishing, and mdworker.
I cannot open the admin console and web publishing is not functioning. I also cannot go to http://localhost:16000/ and get any sort of response.
Just found this, which solved the console opening issue and may help you if you have the same Java version:
However my web publishing engine still will not start! Help please!
I just noticed FileMaker has updated the below instructions since my last post and following the instructions now will resolve the issue completely.
So much closer with this the steps from this wonderful article. I got the FMS12 Start Page to open in a web browser, got the admin_console_webstart.jnlp file to download and when I click on it, I get the following message: "Admin Console Could Not Start: Admin Server Manager unavailable.". Any ideas to fix this last step?
By the way, thank you for that getting me this far, Jason!
The fix on the article resolved my problem.