Not sure I am going to be any help, but I will try.
I do not have any issues getting alerts and not only does my Alert count advise me of how many, I get a pop up, bottom left hand side of screen, to advise that I have an alert.
I do not think this happens while I am in the actual thread the alert is related to. I would have to test that because I do not ‘linger’ in threads for a long period of time.
I have, however, noticed that I am alerted that there are new posts in a watched thread I am reading.
Alerts happen for me automatically after a number of minutes or I can get them by refresh.
Granny, it might help troubleshooting if you can advise what browser you are using?
I am using Chrome on a Windows 7 machine.
These three came in while I was typing this draft without me actually doing anything: