I"m not sure if this is a result of changes made on Friday or even if this is the place to post this.... but I've noticed and anomaly that started about 24 hours ago.
If I am in the game, I get notices of new messages posted in the threads I subscribe to, but if I log out and come back later my message cue does not blink.
This started on Sunday, EST, and I also had an issue whenever I posted in a thread, the background would change on all of the messages of that thread, and it would scroll to the top of the thread. This seems to have cleared up today.
I know the message cue not working is not limited to one computer, as I used two different systems at two different locations (home and work) to login and the result was the same. I also had my wife check hers, and she got the same results.