I don't know if this is related but something seems to have changed in the way pybitcointool serializes scripts since I was working with this around:
https://github.com/vbuterin/pybitcointools/commit/87aaf6dc3f38d853dd8cb324a4eaf72ae309d322
...which I think is still the version you get if you do
pip install pybitcointool
(This is before the name changed to "bitcoin".)

I haven't had a chance to get to the bottom of this and it may be that the old version is broken and the new one is right, but you might like to try comparing what you get with the old version.