Sorry for such a late answer (if it can be considered that) but I found this link that discusses what may be happening to you:
https://github.com/phn/pytpm/issues/3#issuecomment-12133978
The idea that if you have some special Doc scraper in your documentation code that is building autosummary documentation after autosummary has already run may be something to look into if you are still having this issue. Although, I’m not sure how much help this will be.
The key from the link is to add: numpydoc_show_class_members = False to conf.py