I don't know if this is relevant to this addon or the alert improvement addon, but I have confirmed that if your browser has a thread loaded and a new reply is posted, you don't get an alert marker. If you click the alert drop down you see the alert, but it is already marked as "Read". This causes a ton of my members to not realize there was a new reply. For members on slow 3G, they tell me they see the alert maker for a second and then it vanishes.
This add-on is amazing. I love everything made by @Xon
But I too have users telling me this is going on.