If you are providing shared hosting sometimes its dangerous to allow custom php.ini because some users uses dangerous functions and allows custom php.ini on servers.
Custom php.ini can be easily disabled via following instructions.
Login to server via SSH.
Open and edit following file
opt/suphp/etc/suphp.conf nano /opt/suphp/etc/suphp.conf
Search for [phprc_paths] and then uncomment (remove the ; from the front) the following lines:
;application/x-httpd-php=/usr/local/lib/ ;application/x-httpd-php4=/usr/local/php4/lib/ ;application/x-httpd-php5=/usr/local/lib/