[eluser]Lovecannon[/eluser]
Well, I bet you have your URI protocol set to AUTO, open your application/config/config.php and change the $config['uri_protocol'] to PATH_INFO, but PATH_INFO is not correctly set if your PHP installation runs on FastCGI, so you could either change PATH_INFO to ORIG_PATH_INFO or add this line to your CI index.php
Code:
$_SERVER['PATH_INFO'] = (isset($_SERVER['ORIG_PATH_INFO'])) ? $_SERVER['ORIG_PATH_INFO'] : '';