I tend to think it was the JS code I had put in it - or at least that in combination with a *high* amount of Passages that the program had to try to transcribe. Looking at the output - the code that I managed to transcribe to .rpy file was fine, so I really think It was the amount of passages or the JS code. I had an array in the StoryInit Passage which could have made the program choke or something.
Somehow I don't really think it's the amount of passages... looking at the code context the "Nonetype" error suggests to me that it's checking for passage content for a particular passage when it doesn't exist (I hadn't thought to check if it exists first... but I can add a validation for that in subsequent updates).