The default settings for alerts were to skip marking as read Alerts that were viewed in the pop up or on the page. While those defaults have been changed, people who have already registered will need to change them themselves.
Go here, scroll down to Alerts page and summary settings, uncheck the first two boxes. Your problem should now be resolved.
Go here, scroll down to Alerts page and summary settings, uncheck the first two boxes. Your problem should now be resolved.