If you use ESC button on the keyboard, the postion of the ship won’t change.
If you use Mouse to click on the Resume button on the screen, the location will be … right on the place where you click (It makes me die when I fighting against Space Crab 2.0). The location should won’t change, it didn’t appear in previous CI.
I understand what are you saying, but I just tested and for me, even if I click with the mouse, the position of the ship doesn’t change. I don’t know why it changes for you, normally it shouldn’t.