Colin,
Thanks for the quick reply, and thanks again for the ChipWhisperer-Lite. Now if only I could get my hands on a bora board… 
I just installed pycrypto using the voidspace windows installer, and verified that the monitor is now showing correct captures. I didn’t realize that WinPython doesn’t come with that as standard! With the divide by zero it seemed to me that the attack stopped whenever that happened, and didn’t recover the key. Since then I fixed the code so it doesn’t happen anymore. If I find any more issues like that I’ll set up an assembla account and send you a merge request.