After testing with KnightofCups, have confirmed notifications are working as intended for him (you have to interact with the notification either by clicking the checkmark that appears on hover, clicking the notification itself, marking all as read, or going into the notifications page and marking the notification as read, to have the notification go away).
Harena, if you're still having issues with them, let me know what you're doing, what you're expecting to happen, and what's happening instead