The first time mw.notify is used on a page, it considers its top offset (and thus when to become fixed) to be whatever the page's current scrollTop is. This results in it not being visible if first used while not being at the top of the page, until you either scroll to the top of the page, or scroll further than you originally were. This remains true for all notifications for the rest of the page's lifetime.
This is caused by the fix for T54659, which hid the notification area before getting its offset. This can be fixed by hiding the notification area after getting its offset.