Ok, so this behavior is extremely peculiar after testing it out.
In Gamemaker, you can modify a borderless window's position no problem. But if "obj_test" is spawned, or if you go to a room with "obj_test", the ability to modify the window's position gets messed up, and will bump very far if you try to modify it, even after restarting the game.
I bound the R key to restart the game AND reset the position of the window:
game_restart(); window_set_position((display_get_width()*0.5)-(window_get_width()*0.5),(display_get_height()*0.5)-(window_get_height()*0.5));
And I bound the Enter key to spawn "obj_test."
It works just fine when "obj_test" is not present. But even if you restart the game, so it doesn't exist anymore, it will only reset the inside of the window to the middle of the original window. (see video)
If you try to spawn "obj_test" after the window has been weirdly offset, it looks like it tries to create the new window at the middle of the original window, and then it crashes.