When you subscribe to a thread, either manually or automatically, it can be setup to not email, email on every post or email once a week.
Those setttings can be done thru the user control panel. BUT they can also be overriden at the time you join a thread. Odds are that is part of the issue. You may have old threads that still have the old setting. You should be able to look at the email title and then click on that thread and then use the "Threads Tool" menu at the top of the thread to change the setting.