You are running with an old copy of letsencrypt-auto that does not receive updates, and is less reliable than more recent versions. We recommend upgrading to the latest certbot-auto script, or using native OS packages.
I believe that message on the older letsencrypt version can be ignored, at least for now it's still compatible with their servers/protocol. As to the subject of this post, you probably accidentally enabled client protection mode for the domain (ie. you edited it as admin and hit save or changed tabs) - that currently has to be corrected in the database, there's not an interface to that setting yet.
