By default, a notification only shows up when a page is loaded. So if a user gains points after the page has finished loading, the user will need to refresh the page. This feature, allows you to show notifications without the need to refresh the page.
Based on the frequency you set, each x number of seconds a script will check if a new notification exists for the current user. If there is one (or multiple) they are retrieved and shown to the user. This can be particularly useful with ajax powered themes.