Solved! I'm posting here in case others have this problem too:
After a bit of testing around, I found out that the problem doesn't happen in the middle, left or upper part, but only in the lower and right part of the window.
The reason behind it turned out, that if you move the mouse all the way down, then you can still move it a few pixels lower. Even though the cursor appears on the last lowest pixel, in reality the game registers it to be lower than that. If you then move your mouse up, the game first moves it through those invisible pixels below the screen, before actually moving the cursor up.
Same thing happens in the right side of the screen. It doesn't happen on the left or top side of the screen. I suspect the reason behind it is that the cursor has its pointer in its top left corner, so if you move to the right, or bottom of the screen the pointer will still move through the width or height of the cursor.
This is especially problematic for two reasons:
_In the Kingdom view, you scroll a lot, scrolling right or down becomes a bit erratic.
_The bottom part contains the buttons in Kingdom view, so you move your mouse there a lot. The right part contains the buttons in County view, so you move there a lot too.
It works correctly in the floppy version.
Solution?
The solution is to restrict the cursor to the 320x200 window (the original resolution of the game).
You can do this using AutoHotKey, which is a free program.
http://www.autohotkey.com/
Here is a script to clip mouse movement:
http://www.autohotkey.com/board/topic/20345-protecting-an-area-of-the-screen-is-it-possible/#entry133444 Just make sure you edit the third line to
ClipCursor( Confine, 0, 0, 320, 200 )
You can also change the shortcut on the first line (the script in the example sets it to Ctrl+F2).
You will have to run the script every time you run the game, but you can set this in a batch file or the script itself.
If you need any further help on how to set up the script, let me know.