Same here, so OP, did you tried to click on the notifications? What browser do you have configured to default browser?
I'm using Safari, it is set as my default browser in the Internet preferences. When I click on a Notification, it just disappears and nothing happens.
I noticed in my console log there seems to be several Facebook errors:
2012-11-03 12:40:16.079 AM SocialPushAgent[5675]: createFacebookNoticationURLFromID - ERROR: 400. Attempting FQL to determine URL for notification event. FQL: SELECT link FROM unified_thread WHERE thread_id IN (SELECT thread_id FROM unified_message WHERE message_id = "m_msg.576c4dbe0c50400af67f7768bc0cdff177"), response: <...>
I wonder if it is a Facebook problem?
Update: my latest notifications for a couple hours ago seem to work again! Indeed this might have been a Facebook backend problem... not sending the proper Notification URL.