CheckPoint Station is meant to be used with a touchscreen (or mouse). By design, you cannot close CheckPoint Station from the screen, to avoid accidental shutdowns by the user. To terminate the program simply press the "X" key on the keyboard. This will bring up the Shutdown Window.
The shutdown window will ask you if "you want to Check-out all remaining Employees and Students?" If you are shutting down for the evening you will want to select "Yes" to this question. If you are shutting down temporarily during the day for some reason then select "No".