What version were you using previously? Different versions of FileMaker Server come with different versions of PHP and that could be part of the issue.
FileMaker Server 15 overrides your earlier PHP.ini settings. You need to go in there and write down all things that you had before that where not standard from FM.
Along the same line as Johan's suggestion, we've found that IIS occasionally decides that the path names to, for example, include files don't work right. We've never been able to figure out why, but if you have your include files in a higher level directory, sometimes it starts working if you simply move them into the same directory as the PHP files.
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Granting permissions on a directory does not automatically grant the same to the files & folders within. I usually go to the dialog for the levels and compare permissions.
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