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Here is a minified test case, which fails as far back as 738:203dc42ec877.
git clone https://github.com/g2p/bedup -b troubleshooting/cffi-py3.3 --recursive
Reproduced (need to run cffi_py33_bug.py several times before seeing it fail).
Thanks! Fixed in 1518e9e97003.
Excellent! Thanks for making a release.