Tried this 2 times, with the same problem.
./certbot-auto --apache -d mysite.com -d www.mysite.com
Congratulations! Your certificate and chain have been saved at /etc/letsencrypt/live/mysite.com/fullchain.pem. Your cert will expire on 2016-08-30....
But when accessed from any browser, mysite.com:
mysite.com uses an invalid security certificate. The certificate is not trusted because it is self-signed. The certificate is only valid for sys.mysite.org Error code: SEC_ERROR_UNKNOWN_ISSUER
sys.mysite.org is the server host name and does not appear anywhere in Apache config files.
Just one virtual host file is at /etc/httpd/conf.d/mysite_com.conf