After upgrading ISPConfig 126.96.36.199 to 3.1 beta2, I have turned on "Let's Encrypt SSL" for a site. After waiting a minute or two, the site always had this option disabled. So I tried this a couple of times, until... I detected that PHP is not running on this site anymore: regardless of site option "Use socket for PHP-FPM" is set to YES, /etc/php5/fpm/pool.d/web1.conf will always have listen=127.0.0.1:9010 in it, even though the corresponding Apache vhost (correctly) tries to use a socket for PHP-FPM. This is client1/web1, all other sites are fine, using socket at all places.