I believe that's the way it currently works unless there has been an update to vBulletin. And why doesn't it make any sense to you? Why send someone email about a thread they're subscribed to when they are active on the site and all they need to do is check the thread?
Well, for a couple of reasons.
For one, just because I'm either looking at something on the site or maybe starting a new topic, I would never think of checking all the threads I'm subscribed to just in case somebody replied.
Patrick is quite active on this site, so I can see him replying to a different thread while someone is replying to this thread and he not getting email notification because of this arrangement.
If one has say a dozen or so subscribed threads, is it really reasonable to expect that person to check each of those threads every time they are on the site just in case someone might have replied to one. That makes no sense to me.
Maybe this is simply why Patrick is not getting notifications.
The other reason is that I don't necessarily close this site when I'm done.
Just now, I received the email notification about your post, I clicked on the link and opened your post and them I was called away.
Came back about 45 minutes later with your post still up.
So in that scenario, I would not have received any email notifications of any subscription that somebody might have replied to during that time.
I also sometimes minimize the web page when I intend to reply soon but just have to finish something else first. Again, the software would consider me "being active on the site", so no email notification for any replies to subscribed threads.
I don't know about other members, although I'm very interested in Mac topics on this site, I don't have the time to check all my subscribed threads each time I go to this site to see if somebody replied.