I'm not 100% certain on this, but the default directory for web pages using FileMaker is /Library/FileMaker Server/HTTPServer/htdocs/. (Image below.) There are a couple of possibilities:
1) The directory you're trying to use isn't in the include path.
2) The directory you're using to serve the web pages can't resolve the relative path because there is no directory such as:
/Library/Server/Web/Data/Sites/Default/Library/FileMakerServer/Web Publishing/publishing-engine/php/mountain lion/lib/php
Suggestion: Host your sites out of the htdocs folder instead of the other tree you have defined. The FileMaker paths are already set up to handle that.
(TO has FileMaker Server 12.)
FileMaker Server 12 has no WebServer directory, FileMaker Server 13 / 14 has.
I assume you're using Apple Server.app, You say the file is properly placed.
The message indicates that the file is not placed in folder '/Library/Server/Web/Data/Sites/Default/'
Are you sure you have placed the file at the correct folder and not at folder '/Library/WebServer/Documents/'
Thanks for your reply - I"m not sure if restarting fixed it or resetting permissions for the web root folder but pleased to report it's now working again.