Thank you for your post.
Is this Mac OS X Server? Even then, FileMaker Server 13 should NOT look elsewhere.
Since you mention "it has resored back to the WebServer folder as in FMS12", are there any remnants of FileMaker Server 12 existing on the Web Server? If so, remove them, and try restarting FileMaker Server 13.
Are you loading your PHP files from another apache directory?
Any other information you can provide may be helpful in narrowing down the cause.