Wrong master php.ini used in fcgi mode with custom config
In fcgi mode, using a custom php configuration, the php.ini file automatically built in /var/www/conf/webN is based on /etc/php5/cgi/phi.ini instead on /etc/php5/fcgi/phi.ini (which is used if no custom config is specified).
In apache2_plugin.inc.php at line 553 is probably missing a test like:
if($data["new"]['php'] == 'fast-cgi') { $master_php_ini_path = $fastcgi_config["fastcgi_phpini_path"]; } else { $master_php_ini_path = $web_config['php_ini_path_cgi']; }