Used to be that when you received new reputation points, your "Notifications" link on the top bar used to light up - then click on it, and it would say either New Reputation Received and/or New Unread Message.
Now, upon receiving new rep, it does not light up.
Can't call this a bug; maybe this site made an intentional change to reduce confusion; I myself was confused a few times when my Notifications link was lit up and yet I had no PM in my inbox; one of the mods (LuJon I think) chimed in saying it was probably new rep; he was right. Then.
But now it no longer works this way.
Platform: Windoze XP/Firefox