are hopefully getting close then but: They both have the same amount of accounts and the same domains?
Thanks for the help in the thread, I backed up and flipped a coin. new domain now retrieved a new ssl with letsencrypt and has both checkboxes checked. tried another domain by turning off ssl and backup and that's worked fine with both checkboxes checked. I just have one domain that does have a current valid cert but both checkboxes are unchecked and won't apply when I check them.
See: https://www.howtoforge.com/community/threads/lets-encrypt-error-faq.74179/ To find out why this happens.