Broken PHP or Apache handler

I have try to install ionCube Loader on my Virtualmin (CentOS 6.6) using Method #2 from http://www.servermom.org/how-to-install-ioncube-loader-on-centos-6/802/ but it looks like switching distro to Atomic made some changes to PHP/Apache configuration.

Right now browsing any vhost on that machine simply wants to download the installation page, instead of opening it in PHP or HTML.

I have found that topic: http://www.virtualmin.com/node/25521 and based on it I was able to get sites back to work running PHP as the mod_php but how can I get back to FastCGI?

Thanks