This only happened recently for me, but now if I sit in the new or unread categories, the unread count never changes.
I do get popups when new notifications arrive, and my avatar gets the number, but that's it.
OS X 10.10, Chrome latest/
Yes, it'd be great if someone could look at this. I have to reload the page or flip to the Unread tab for it to discover that I indeed have one or more unread messages.
Confirmed, something is broken here ... having a look.
I could be wrong but I seem to be getting the same problems with the 'new' count too
The fix is deployed here, try it out 
Yay 