Let's say I'm watching a thread, and I get an email notification that the thread has been updated. If I click on the link in the email, which takes me to the latest unread post, the alert should automatically clear. Clicking on the link implies that I have been properly alerted, and clicking on Alerts all the way at the top is redundant.
Despite being marked as read, I have users who stop receiving alerts for threads that they are subscribed to or tagged to. My assumption is that this happens because the user accessed the thread through some method other than clicking on the alert.
It's unrelated to alerts. They need to read the thread - if there is already a new (unread) post in the thread, then they won't receive an alert again until they're caught up. They can see the list of such threads on the "watched threads" page. Alternatively, they can just mark all forums as read.
Well you mentioned people watching threads, so that's what I was responding to. Regardless, it'd probably be better to post a thread in troubleshooting (this is a suggestion thread and generally unrelated) explaining the situation in more detail.