fgci uses different php.ini
using fast-cgi. if no custom php setting is defined for a web site the .php-fcgi-starter set PHPRC=/etc/php5/fcgi/ and the php.ini is loaded from here.
if a custom php setting is defined for a web site the .php-fcgi-starter set PHPRC="/var/www/conf/web6", but the php.ini file built in /var/www/conf/web6 is derived from /etc/php5/cgi/php.ini as configured in server config option [CGI php.ini path].
Perhaps should there be another server config option [Fast-CGI php.ini path] = "/etc/php5/fcgi/php.ini" or the php.ini file built in conf directory should be always derived from /etc/php5/fcgi/php.ini.