I've noticed in the past few hours that comment replies are not causing the notification red dot & number to show up. However, on my account page, the red square counter on the Responses tab does show up, and after clicking on the Stack Exchange button and going to my inbox, I see the comment reply there.
I haven't noticed / checked yet whether this is occurring with any other class of events that normally creates a notification red dot. (Edit: I just got the Civic Duty badge on TeX.SE, and the pale blue dot notifying of a new badge is working for me.)
Is anyone else seeing similar behavior?
I'm using Chrome 26.0.1410.64 m on Windows 7 Home Premium 64-bit.