They do not consistently appear in their designated place and as a result eventually as you kill more bosses they push other loot notifications (self looted) and other loot rolls up towards the top end of screen, sometimes even off completely.
Newly created bonus loot frames will also cause a large area of the middle screen to become uninteractable and unclickable once they are gone. The clicks are registering, but it is as if an invisible overlay is created on parts of the screen which absorbs all the mouse clicks. For example if you try to click a NPC or hold RMB to rotate the camera around, nothing will happen. Meanwhile, the edges of the screen register all mouse events just fine.
The only solution is to reload ui, often based on severity and quantity of boss kills / stacked frames a relog is required. Once a full column is created, the frames will no longer originate near the bottom middle of the screen but instead closer to the top each time.