Hi Aimee,
Can you test this to close the course window:
Insert 2 buttons or smart shape used as buttons (as Finish course buttons).
On the first button apply an action to execute javascript and in the script window, use this script: parent.close()
On the second button apply an action to execute javascript and in the script window, use this script: top.window.close()
Upload the published project on your LMS and check if any of these works for you.
Thanks
Himanshu