Alerts are only generated for the first reply since you last read or marked as read the thread in question. No more alerts will be generated until you then go and read or mark read the thread.
This is by design. While alerting for every single reply might be ok for low traffic threads the cost of alerts, especially those which also generate mail would grows very quickly in a busy thread with lot's of subscribers.
This behaviour is hinted at in the alerts themselves where it states there may be more posts after this, implying only the first reply is responsible.
This seems to explain things from your descriptions above.
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As a bonus note (since it comes up often and people might end up here if the search the feedback forum), user tagging is independent from the thread subscription alert generation. Tagging a user in a new post will always generate an alert for them. However editing a post to add new tags will not, as this would require maintaining the entire history of all tags in all posts forever.
With that in mind if you are trying to maintain a conversation with someone through a thread it's always a good idea to tag them in the replies you direct to them, with the possible exception of the thread starter who by default will be subscribed to their own thread unless the choose otherwise.
