Set the mime type check in the Upload class to reference the global mimes variable.
diff --git a/system/libraries/Upload.php b/system/libraries/Upload.php
index 1225ee3..23e52e4 100644
--- a/system/libraries/Upload.php
+++ b/system/libraries/Upload.php
@@ -821,9 +821,11 @@
 	 */	

 	function mimes_types($mime)

 	{

+		global $mimes;

+	

 		if (count($this->mimes) == 0)

 		{

-			if (@include(APPPATH.'config/mimes'.EXT))

+			if (@require_once(APPPATH.'config/mimes'.EXT))

 			{

 				$this->mimes = $mimes;

 				unset($mimes);