The issue is probably because you let FMS install PHP for you instead of doing it manually. Therefore now it is using a mix of settings and is generally not optimized for proper testing. Your best bet is to grab the installer from http://php.net
and install that copy. However you will have to delete/rename the PHP ini from the FMI folder to prevent it from loading, specifically rename/delete this file:
C:\Program Files\FileMaker\FileMaker Server\Web Publishing\publishing-engine\php\php.ini
Then install the installer version, modify the PHP ini for correct temp folders, and hten copy it into C:\Windows. Once done restart IIS and it should work better.