I too noticed the LEDs no longer flashing.
In the Look and Feel section there are a number of Notification settings. (It was not easy to find them; they ought to be under Message Notifications.)
I turned off Notification icon during sync and push, and Notify about ongoing operations, and the LED came back.
Also in Message Notifications, is there a setting to turn sound notifications off? I couldn't find one, so made a silent WAV file and am using that.