This is my experience, it's happened to me twice, and I'm wiser for the experience that I'm sharing here.
We know that FileMaker Server gets installed AFTER the OS-X Server app is installed and launched and configured. However I think it's not as well known that when Apple distributes an update to OS-X that includes an update of their Server app, it can require uninstall and re-install of FileMaker Server.
Here's the scenario.
The machine is a Mac Mini Server that was, until Saturday, running OS-X 10.9.4. Apple released 10.9.5 together with a new copy of Server 3.2.1. Filemaker Server 12.06 was until that time running perfectly. However after the update of the OS-X Server app, there was no response from any PHP pages and the reported error was #22, with a message indicating that the user did not have the PHP extended privilege.
Uninstalling FileMaker Server, restarting the machine, and then re-installing FileMaker Server didn't do any good. In fact, it made it worse because the Server Deployment could see Apache but it could not connect with it.
This is what worked:
Make screen shots of all the OS-X Server settings because there is no way to save those settings.
Trash the Server application.
Trash the directory Library/Server
Uninstall FileMaker Server with the usual way of protecting the databases, extensions, preferences, settings, plug-ins, etc.
Download OS-X Server app from the App Store
Launch OS-X Server app and configure
Conclusion: I don't know what causes the issue to occur but I suspect there is some PHP code written by the updated Server app that over-writes the FileMaker PHP code.
One other note: after the reinstallation of FileMaker Server, the admin console refused to launch on the first attempt, but from a remote machine it launched and ran successfully. Thereafter, the admin console ran fine on the server locally.