It's not that simple that you just didn't register different points for the different orientations?
Say that you use the camera with C.Fn III-12-0. That means that if you select the top AF point and turn the camera around, you still have the same point active, so it's now out on one side.
Now you change to C.Fn III-12-1. If you select the top point when holding the camera in landscape orientation, you don't get the top point again just because you turn the camera vertical (with grip up). In that vertical position, you have to move the selected AF point to the top (which is equivalent to the camera's rightmost point, when held normally).
Now, when you go back and forth betwen horizontal and vertical, grip up, you'll get the top point all the time, as you set it like that.
But still, if you go vertical the other way (grip down), once again you don't have the top point (camera's leftmost AF point) active, as you haven't selected that with the camera in that orientation yet. Move the point to the top, while still holding the camera vertical in that direction, and finally you have it set to use the top one in all three orientations.
The same goes for the registered home point. You have to select and register one such point in all three orientations for that to work, or the camera will consider the center point to be your home point (HP).