We are using Windows 7. But I guess you too. On both computers where I updated Rhino to SR12 we got that problem. I stopped updating the 5 remaining computers yesterday because I am afraid it will be same there then. Is there maybe a communication progress between Python/Rhino and something else that could be blocked by a software we have installed? - but I think that would cause an error message.
Is there a way to downgrade to SR11 in case of emergency?
Or maybe I could change the script in layer.py so it works the way your second script does - but that seems dangerous to me.