Hi Ben,
The Notes window will disappear when it is empty. There is probably a space or tab in the window that you cannot see. Select everything in the window (ctrl-a), delete it (ctrl-x), and then close the window using the 'X" at the top right corner or navigate to another page and back.
You can find instructions for this and other similar tasks in the Reference section of SAM's Help system.
Best regards,
Paul.