FileMaker has stated that FileMaker Server 14 on OS X is not compatible with Server.app installed (OS X Server). For security on any server it is good practice to keep the machine "logged off". It is also good practice with FileMaker Server to use external disk drives for backup. On standard OS X without Server.app installed external disks are dismounted when the user logs off which means that the drives that FileMaker Server needs to back up onto become unavailable.
Fortunately there is an easy fix if the problem occurs which is to enter the following command into OS X terminal.
sudo defaults write /Library/Preferences/SystemConfiguration/autodiskmount AutomountDisksWithoutUserLogin -bool true
My suggestion is that the installation of FileMaker Server on OS X should include this command as a part of the install.