Thank you for taking the time to research and explain that.

It's funny, but on my code example, I got it to happen every time and you said it didn't happen unless you made the change to use root.update() and root.destroy().  I tried it out again and realized that I was closing the tk window before OutputWindow every time, thus I was getting the warning using root.mainloop().  Of course, if I close OutputWindow first, I don't get the warning.  That's running from the command line.

I suppose this issue needs to be split into the real bugs that you mentioned.  It seems to be at least 2 or 3 different things to look at (EditorWindow and EditorFrame and CodeContext).  I'll delete the current PR for this issue.  

Thanks!