There are several factors that influence alert behavior:
- Whether the alert is marked "read"
- Whether you have persistent alerts enabled
- If and and how you've chosen to summarize alerts
You can mark alerts read in two ways: by actually viewing the new content/clicking through the alert, or simply by
viewing the alert itself.
If you want the alert to remain up until you actually see the new content for yourself, check the box labeled "alerts pop-up skips mark read." Otherwise, you'll want the alerts pop-up to automatically mark everything as read for you so that you won't miss alerts. (This seems to be the case for people wondering why they aren't getting new alerts for threads they're following.)
Persistent alerts also helps users avoid missing alerts. Here's how that feature is described:
"If enabled, you will be alerted/emailed (based on your settings) for every post in a watched thread as long as you have no unread alerts for that thread. If disabled, you'll only be alerted for new posts since the last time you viewed the thread."
If you summarize alerts, then if 20 new posts were added since your last visit, the alerts pop up will group those together into a single entry.
And you can now customize push/email alert behavior for each different interaction type. Let's say you want to receive site alerts for all new replies to watched threads, push notifications every time someone mentions you - but you only want email notifications if you get a new private message. You can do that.