Instead of doing file name security for Enable Query Strings, I am using the already existin _filter_uri()
diff --git a/system/libraries/Router.php b/system/libraries/Router.php
index e2a1480..6af6ad3 100644
--- a/system/libraries/Router.php
+++ b/system/libraries/Router.php
@@ -49,7 +49,6 @@
 	function CI_Router()

 	{

 		$this->config =& load_class('Config');

-		$this->input =& load_class('Input');

 		$this->_set_route_mapping();

 		log_message('debug', "Router Class Initialized");

 	}

@@ -71,11 +70,11 @@
 		// If so, we're done since segment based URIs are not used with query strings.

 		if ($this->config->item('enable_query_strings') === TRUE AND isset($_GET[$this->config->item('controller_trigger')]))

 		{

-			$this->set_class($_GET[$this->config->item('controller_trigger')]);

+			$this->set_class(trim($this->_filter_uri($_GET[$this->config->item('controller_trigger')])));

 

 			if (isset($_GET[$this->config->item('function_trigger')]))

 			{

-				$this->set_method($_GET[$this->config->item('function_trigger')]);

+				$this->set_method(trim($this->_filter_uri($_GET[$this->config->item('function_trigger')])));

 			}

 			

 			return;

@@ -483,7 +482,7 @@
 	 */	

 	function set_class($class)

 	{

-		$this->class = $this->input->filename_security($class);

+		$this->class = $class;

 	}

 	

 	// --------------------------------------------------------------------

@@ -510,7 +509,7 @@
 	 */	

 	function set_method($method)

 	{

-		$this->method = $this->input->filename_security($method);

+		$this->method = $method;

 	}

 

 	// --------------------------------------------------------------------

@@ -542,7 +541,7 @@
 	 */	

 	function set_directory($dir)

 	{

-		$this->directory = $this->input->filename_security($dir).'/';

+		$this->directory = $dir.'/';

 	}

 

 	// --------------------------------------------------------------------