/etc/torrc.d/*.conf / /usr/local/etc/torrc.d/*.conf support might be causing issues.
If that is the case it can be solved by adding to documentation to manually run torrc-d-cleaner before restarting Tor or perhaps a usability tool which does both (run torrc-d-cleaner + restart Tor).
On top of that anon-verify has a bug and does not show all config files which makes debugging for users harder. I am working on it.