@armensano, if this is an issue with certification, your best course of action is to email email@example.com. The certification team will then look into the incident and reply to you directly.
Just to make sure we are clear on your ask here.
You have a secured NiFi and NiFi-Registry installation that uses user/client certificates to authenticate your user via the mutual TLS handshake?
If that is the case, you should not be seeing a NiFi/NiFi-registry login window.
Can you share screenshots?
What do you see in the nifi-user.log when you attempt to access NiFi?