Index: wp-includes/update.php
===================================================================
--- wp-includes/update.php	(revision 8339)
+++ wp-includes/update.php	(working copy)
@@ -120,6 +120,10 @@
 			$plugin_changed = true;
 	}
 
+	foreach ( (array) $current->response as $plugin_file => $update_details )
+		if ( ! isset($plugins[ $plugin_file ]) )
+			$plugin_changed = true;
+
 	// Bail if we've checked in the last 12 hours and if nothing has changed
 	if ( $time_not_changed && !$plugin_changed )
 		return false;