The installation procedure of ISPConfig modifies the PHP settings for Apache(2). It removes the standard allowed php execution. Otherwise you could not select to switch php on or off for a website. If you want to run PHP, you have to set the PHP tick box for every website you want php to work on. Maybe you created a website yourself in the main apache2.conf? If that's true, you should leave the creation of sites and apache configurations to ISPconfig. Just thinking out loud.
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