copy the system/classes/kohana/request.php to your application/classes/kohana/request.php directory and open the file.
edit the file at around line 332 in the detect_uri method.
public static function detect_uri()
{
...
// cut out the initial base part to make sure the internal routing will get correct input
$uri = str_replace(Kohana::$base_url.Kohana::$index_file, '', $uri);
return $uri;
}