This is a message from website, not the browser. Like I said before, JS is used to do various things automatically.
In SuperUser, it is used for instance for refreshing thread contents while you browse. Browser sends asynchronous request to SU to check if some new answers were posted every few minutes, and if so, it displays a message in top of a page asking if you want to load new answers.
- Via add-ons like WebDeveloper
- Adding a button after installing Toolbar buttons
and also probably other numerous add-ons.
It's strange you tell it is already enabled. Maybe some other add-ons affect the setting (most notably, NoScript).