Removing .php extension gives 404

After spending several hours, going through the entire CodeIgniter scripts, I found a hack. Not ideal, but works fine for me.

Under system/URI.php, within the public function __construct(), based on current full URL, I switch between $protocol = 'REQUEST_URI' and $protocol = 'QUERY_STRING', when the URL includes and does not include the name of the application's folder, respectively.