Having been testing out the new notification of new topic posts, I noticed that it was sometimes losing my topic notifications. It turns out that the Quick Reply mod had a bug in it and it was trying to check whether you were subscribed to the topic on a value that was never set. This means that if you subscribed to a topic and then posted using the Quick Reply box, your notification will be lost.
This problem has now been fixed, and any more posts using the Quick Reply box should now keep your current notification status.