Hmmm, the way the email notification act is this.
You subscribe to a thread, either by posting to it, or by clicking the "Watch This Topic" link at the bottom of a thread. After subscribing (or watching) a thread/topic, you will receive 1 email from the site when the next reply is posted (if email notification is selected in your profile), no further email will be received about that thread until you visit the site AND you visit that particular thread you received the email about. This is the only negative about having the message in the email, you may not visit the topic, cause you already read what was in the message.
One thing to be careful, there are two links in each email, on to visit the thread, and 1 to unsubscribe (or Stop Watching) the thread, ht the wrong link and no more email about that thread
It sounds like for whatever reason you did not visit the topic after an email was sent to you. This could be cause you didn't receive the original email or the reason stated above, or whatever other reason. At any rate, I am glad that it has started working for you