Have you checked the PHP.ini file?
When you installed the new server a default PHP.ini file gets installed. I use a text editor like BBEdit to side by side compare the old and new files.
There are quite a few differences as it is a different version of PHP and the directory structure for the web server is also different. However the only relevant differences I can see are the include path (which has been set correctly), various options to do with logging and options concerinig other databases (MySQL and SQLite).
Further information about this problem:
The same application code running on the same web server (now Apache 2.4.16 with PHP 5.6.14 running on Windows VIsta) shows the same problem when using an FMS13 server (and the FMS13 PHP API) but works correctly when using an FMS11 server (and the FMS11 PHP API). The only code difference apart from the PHP API is using a different server adderss to point at the server running the othe version of FMS.
Conclusion: There must be a bug in FMS13 or the FMS13 PHP API.