I just installed I-MSCP and everything works fine so far (Except for the old Ajaxplorer 4.2.3 currently using but I saw that the RC5 milestone has the Pydio (former Ajaxplorer) 5.0 on the list so that would be very cool.)
I am using 1.1.0-rc4.6 with PHP-FPM and php.ini per domain.
So what I found out that when logged in as Admin, and I change the Value for the disable_functions directive, noting happens. Not one line in /etc/php5/fpm/php.ini nor in /etc/php5/fpm/pool.d/master.conf nor in /etc/php5/fpm/pool.d/domain.conf. When I delete for example the "phpinfo" from the php_admin_value[disable_functions] line in the /etc/php5/fpm/pool.d/domain.conf, it works. But from the admin panel, nothing works.
So I think it is a bug but I am not sure, that's why I am asking here first.