Thank you for the post.
FileMaker Server 13 and the 10.9 or 10.10 OS X Server.app should not be run on the same computer because the two are not compatible. The Server.app is not needed because FileMaker Server 13 configures our instance of a Web Server during installation and deployment.
As a test, if you uninstall the Mac OS X Server.app and uninstall and reinstall FileMaker Server 13, then does this still occur?
A similar issue was reported in the following thread:
For additional information, please review the following knowledge base article: