While installing a 3rd party application on one my client's sites today, I needed to change the PHP config settings.
I noticed there was a ini.php in the top level directory of the user account. However, when I made changes to it, nothing happened.
Turns out - php.ini is for configuring PHP 4. To configure PHP 5, you need to upload php5.ini. This is described here.
D'oh - I was so close, yet so far away.