Let’s Encrypt is not trusted in Tor Browser 5.5.2 so don’t know how your pipes are to Tor but maybe idea to open ticket there.
Works fine for me. Perhaps you are checking on a site where the certificate is not set up correctly ?
Certificate’s are set correctly before I always had a A+ on https://www.ssllabs.com/ssltest/analyze.html?d=cyberguerrilla.info now I see “Chain issues” in the “extra download” of Let’s Encrypt Authority X1
Presumably you have changed something - renewed your certificate ? and not copied the full chain of certificates into your config.
Don’t ignore the obvious: a possibly rogue exit node.
In this case you can tell either by checking with a standard browser, or ssllabs - there is no chain provided.
A “Chain issues”/“extra download” is a big problem : if your visitors don’t have the chain in their cache (if they didn’t visits a correctly set up website using let’s encrypt), the connection will appear not trusted ! It’s not lined to tor specifically.