Thank you for your post.
I am unable to replicate the issue with FileMaker Server 14.0.4a under Mac OS X 10.11.1 and Mac OS X 10.10.5. I currently don't have access to Mac OS X 10.9.5.
In each case, I am able to start and stop the server from the command line using:
fmsadmin start server
fmsadmin stop server
Since the command "fmsadmin" isn't being recognized, something in the installation didn't update properly. Therefore, I would uninstall FileMaker Server 14.0.4a, move the relevant files (database files, etc.) to the Desktop, remove the FileMaker Server folder, and then reinstall FileMaker Server 14.0.4a.