Index: bp-messages-notifications.php
===================================================================
--- bp-messages-notifications.php	(revision 7663)
+++ bp-messages-notifications.php	(working copy)
@@ -154,7 +154,7 @@
 		foreach ( (array) $message->recipients as $recipient ) {
 			bp_notifications_add_notification( array(
 				'user_id'           => $recipient->user_id,
-				'item_id'           => $message->id,
+				'item_id'           => $message->thread_id,
 				'secondary_item_id' => $message->sender_id,
 				'component_name'    => buddypress()->messages->id,
 				'component_action'  => 'new_message',