While traveling around, I noticed that my map was not centering itself properly on the correct map.
Here, you can see the problem.
First, the map is just in my hand:

Everything looks normal and how it should be. No problems here.
But when i put it away so that i get the onscreen minimap it looks like this:

If i set the zoom multiplier to 2.0 instead of the standard 1.0 and set show map boundries to true it will look like this:

This seems to tell me that even though the map in the atlas in the hand seems to know which map to display, when it comes to the minimap, it seems to show the bottom half, which I haven't even mapped yet or even activated as an empty map yet.