I've been wandering through hell last night/this morning as I upgraded my system from Ubuntu 14 to 16 and my ISPConfig install (just a minor patch iirc). I feel that I'm really close, but I'm stuck on what I hope is the final stick in my spokes. This has been after setting my system to use PHP 7 in the ISP server configs.
Not sure what the issue is, but: do you have suexec enabled for the site? what are the ownership/permissions on /var/lib/php7.0-fpm/web1.sock?