I have the opposite problem. The threads I get email notifications for that get new replies are filling up my mail box. Used to be you would get 1-2 mails to replies and they would stop until you visited the thread. Now I get a mail for EVERY reply, can get annoying having to delete are that mail especially when the threads get very active.
That's because notifications and the notification settings I linked were added with the upgrade. What you're receiving is supposed to happen based on the settings you have selected.
In your case you need to change "Immediate" to either "Daily/Weekly Digest".