So that happened... I had just posted 3.6b2 earlier this week, and was quickly informed that it was terribly broken. The process works!
The very popular nose coverage plugin uses the coverage.py API in a way that I wasn't testing, shame on me! Now I have a test of that style, to prevent this in the future.
The good news is that coverage.py 3.6b3 fixes the problem. I'm not planning any more changes for v3.6. Try it and let me know if you find any problems.
Thanks, and sorry for the version-churn.