In https://github.com/pypa/setuptools/issues/836, I've pinpointed this commit as implicated in dictionaries spontaneously losing keys. I have not yet attempted to replicate the issue in a standalone environment, and I'm hoping someone with a better understanding of the implementation can devise a reproduction that distills the issue that setuptools seems only to hit in very specialized conditions.

Please let me know if I can help by providing more detail in the environment where this occurs or by filing another ticket. Somewhere we should capture that this is a regression pending release in 3.6.0b3 today, and for that reason, I'm adding Ned to this ticket.