Even though this is technically a separate issue, I'm posting this here because once I started receiving my notifications again, I kept thinking there was still a problem... and was worried they might even stop again. So I've been doing this since the notifications started up a few weeks ago.
If for example a certain thread I subscribe to happened to get 3 new messages each day. On the first day I get notified of 3 new messages... I click the link, read all 3, and exit. On the second day, I get notified of 6 new messages... I click the link, only 3 are new, and the other 3 are from the previous day. The next day it's 9 new messages... and again only 3 are new. This continued as long as the new messages were on the same page. Once I went to the next page, it started over.
That explanation may not be precisely accurate but you get the idea. Since then, I've developed a habit of clicking on the link below the last post on the page... in this case it would have shown "3 Unread Posts" for example. Clicking on it resets the counter and changes it to "0 Unread Posts". Since I started doing that, everything has been perfect... and it's nice to be back.