With fast-cgi, custom php.ini needs to be in the cgi-bin folder.
1) Move php.ini to cgi-bin folder
2) In cgi-bin folder, create php.fcgi and put the following in this file:
#!/bin/sh export PHP_FCGI_CHILDREN=1 export PHP_FCGI_MAX_REQUESTS=10 exec /usr/local/cpanel/cgi-sys/php5
3) chmod php.fcgi to 755.
4) Upload .htaccess under public_html, put the following:
AddHandler php5-fastcgi .php Action php5-fastcgi /cgi-bin/php.fcgi