I use nginx/1.8.0 + PHP 5.6.9-0+deb8u1. Standard installation.
Assembly and installation Phalcon done through github.com. The current version Phalcon is 2.0.6.
When I connect extension Phalcon via /etc/php5/fpm/pool.d/site.conf как php_admin_value[extension] = phalcon.so — I have an error.
When I connect extension Phalcon via /etc/php5/fpm/conf.d/30-phalcon.ini — OK.
How it works you can see on the video — https://www.youtube.com/watch?v=GdIuKleA12o&feature=youtu.be
P.S.: Sorry for my English.