http://ravenphpscripts.com/faq-2-.html#39
This is usually the result of your theme not using the latest security feature(s)in the latest patches.
In your theme.php find:
if ($index == 1) {
and change to:
if (defined('INDEX_FILE')) {
Also make sure that your modules have define('INDEX_FILE', true); if you want the right blocks to appear.