Looks like I seem to have finally acquired the notorious "1 Notification" bug as well, simply by opening two new PMs I had in new tabs at the same time.
For me it's the Mark Unread button not working right. I have no unread messages but my inbox says otherwise and I'm stuck at 40 notifications.
Spoiler:
I was playing about in my inbox last night. Select All'd and Mark Unread'd some messages, and did it multiple times to the same bunch of messages to see what would happen. Notifications went up by 20 each time I did it. Some Notifications disappeared after I opened the messages but the "duplicate" notifications remain.