I don't know why you're not getting alerts for watched threads or threads in watched forums if your Alert Preferences are properly set.I don't always receive email notifications either. Nor do I always get alerts to threads on the actual site, and often find myself happening upon additional posts by pure chance. This would be ok if it weren't for the fact that I seem to sometimes miss being made aware of the thread starter's new posts in threads that I've been involved in for a long time (or even a short time, come to think of it). I feel a wee bit negligent for not noticing updates.
Email notifications work differently. When someone replies to a thread you're watching, you should get an email notification, but you don't get any further emails for that same thread until you log in and read the thread.