I think there is possibility you can select your server's php or Filemaker Server's PHP, I will share my personal experience, When i was using FileMaker Server 10 , it was php 5.2 that comes with Filemaker server 10, but my mac server had php 5.3 . I select to use Server's php instad Filemaker's PHP, But i did not see any results. Then i reinstalled FMS select FMS php , after that some how it worked.
** But I already had some web sites that was using php(5.3). those web sites got messy in the client browsers(this happen only when ever i installed FMS, when i remove fms web sites working fine). That time i was not able to fix the issue my own. But latter that i found you can change php.libso file from Mac server admin .
So make sure you have backup.