When running PHP through PHP-FPM you have option to chroot FastCGI PHP server. Unfortunately, Apache is not aware of chrooting and therefore pass wrong script path to the server.

This patch supposed to help with it - http://orfika.net/src/mod_fastcgi-chroot-patch/

Below are steps I've run in order to apply this patch to my server. First, you want to remove installed mod_fastcgi package: