As explained in my lengthy post on the question authors' forum, I find it confusing that question prototypes have two identically named fields "Question type". One is under "CodeRunner question type" and specifies the prototype that the current question makes use of. The other is under "Advanced customisation" and specifies the name for the prototype being created if "Customize" is checked and "Is prototype?" is set to "Yes (user defined)".
I suggest renaming the latter to something like "Prototype name". Maybe leaving the text field blank instead of loading the original question type would be helpful as well.