Problem adding new Let's Encrypt certificates

Hi. I can't get let's encrypt to work for my new website, can anyone help point me figure out what I am doing wrong?

I have IspConfig 3.1.13
Webserver: nginx
I have replaced the domain name for my actual site with "mysite" below.

I have 10+ webservers running working let's encrypt certificates, but now when I try to add a certificate to a site the check boxes are unchecked when I get back to the configuration.
.
I have checked the letsencrypt logs after running "certbort certificates" and it reads:
------------
Certificate Name: mysite.com-0001
Domains: mysite.com
Expiry Date: 2019-10-03 11:40:00+00:00 (VALID: 89 days)
Certificate Path: /etc/letsencrypt/live/mysite.com-0001/fullchain.pem
Private Key Path: /etc/letsencrypt/live/mysite.com-0001/privkey.pem
Certificate Name: mysite.com
Domains: mysite.com www.mysite.com
Expiry Date: 2019-10-03 11:15:06+00:00 (VALID: 89 days)
Certificate Path: /etc/letsencrypt/live/mysite.com/fullchain.pem
Private Key Path: /etc/letsencrypt/live/mysite.com/privkey.pem
---------

I followed the instructions to run the server.sh and this is the output:
----
05.07.2019-14:39 - DEBUG - Calling function 'check_phpini_changes' from plugin 'webserver_plugin' raised by action 'server_plugins_loaded'.
05.07.2019-14:39 - DEBUG - Found 1 changes, starting update process.
05.07.2019-14:39 - DEBUG - Calling function 'ssl' from plugin 'nginx_plugin' raised by event 'web_domain_update'.
05.07.2019-14:39 - DEBUG - Calling function 'update' from plugin 'nginx_plugin' raised by event 'web_domain_update'.
xfs_quota: cannot set limits: Function not implemented
xfs_quota: cannot set timer: Function not implemented
05.07.2019-14:39 - DEBUG - Create Let's Encrypt SSL Cert for: mysite.com
05.07.2019-14:39 - DEBUG - Let's Encrypt SSL Cert domains: --domains mysite.com
which: no letsencrypt in (/root/.local/share/letsencrypt/bin)
which: no certbot in (/opt/eff.org/certbot/venv/bin)
05.07.2019-14:39 - DEBUG - exec: /bin/letsencrypt certonly -n --text --agree-tos --expand --authenticator webroot --server https://acme-v02.api.letsencrypt.org/directory --rsa-key-size 4096 --email [email protected] --domains mysite.com --webroot-path /usr/local/ispconfig/interface/acme
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Plugins selected: Authenticator webroot, Installer None
Starting new HTTPS connection (1): acme-v02.api.letsencrypt.org
Obtaining a new certificate
05.07.2019-14:40 - DEBUG - Let's Encrypt Cert file: does not exist.
05.07.2019-14:40 - DEBUG - SSL Disabled. mysite.com
05.07.2019-14:40 - DEBUG - Writing the vhost file: /etc/nginx/sites-available/mysite.com.vhost
05.07.2019-14:40 - DEBUG - Writing the PHP-FPM config file: /etc/opt/remi/php72/php-fpm.d/web26.conf
05.07.2019-14:40 - DEBUG - Calling function 'restartPHP_FPM' from module 'web_module'.
05.07.2019-14:40 - DEBUG - Restarting php-fpm: systemctl reload php72-php-fpm.service
05.07.2019-14:40 - DEBUG - nginx status is: running
05.07.2019-14:40 - DEBUG - Calling function 'restartHttpd' from module 'web_module'.
05.07.2019-14:40 - DEBUG - Checking nginx configuration...
05.07.2019-14:40 - DEBUG - nginx configuration ok!
05.07.2019-14:40 - DEBUG - Restarting httpd: systemctl restart nginx.service
05.07.2019-14:40 - DEBUG - nginx restart return value is: 0
05.07.2019-14:40 - DEBUG - nginx online status after restart is: running
05.07.2019-14:40 - DEBUG - Processed datalog_id 754
05.07.2019-14:40 - DEBUG - Remove Lock: /usr/local/ispconfig/server/temp/.ispconfig_lock
finished.

----
I also ran the common-issues script, output as follows:
---
> [INFO] ISPConfig is installed.
> [WARN] /usr/local/ispconfig/server/lib/config.inc.php is missing.
>
> ##### VERSION CHECK #####
>
> [INFO] php (cli) version is 7.1.30
>
> ##### PORT CHECK #####
>
> [WARN] Port 465 (SMTP server SSL) seems NOT to be listening
>
> ##### MAIL SERVER CHECK #####
>
> [WARN] I found no "submission" entry in your postfix master.cf
> [INFO] this is not critical, but if you want to offer port 587 for smtp connections you have to enable this.
> [WARN] I found no "smtps" entry in your postfix master.cf
> [INFO] this is not critical, but if you want to offer SSL for smtp (not TLS) connections you have to enable this.
>
> ##### RUNNING SERVER PROCESSES #####
>
> [WARN] I could not determine which web server is running.
> [WARN] I could not determine which mail server is running.
> [WARN] I could not determine which pop3 server is running.
> [WARN] I could not determine which imap server is running.
> [WARN] I could not determine which ftp server is running.
>
> ##### LISTENING PORTS #####
> (only ()
> Local (Address)
> [localhost]:10024 (-)
> [localhost]:9000 (-)
> [localhost]:10025 (-)
> [localhost]:10026 (-)
> [localhost]:10027 (-)
> [localhost]:9070 (-)
> [anywhere]:110 (-)
> [localhost]:9071 (-)
> [anywhere]:143 (-)
> [anywhere]:8080 (-)
> [anywhere]:80 (-)
> [localhost]:9072 (-)
> [anywhere]:8081 (-)
> [anywhere]:8082 (-)
> ***.***.***.***:53 (-)
> [localhost]:53 (-)
> [anywhere]:21 (-)
> [anywhere]:22 (-)
> [anywhere]:25 (-)
> [localhost]:953 (-)
> ***.***.***.***:443 (-)
> [anywhere]:993 (-)
> [anywhere]:995 (-)
> *:*:*:*::*:10024 (-)
> *:*:*:*::*:3306 (-)
> *:*:*:*::*:10026 (-)
> [localhost]10 (-)
> [localhost]43 (-)
> *:*:*:*::*:8080 (-)
> *:*:*:*::*:53 (-)
> *:*:*:*::*:21 (-)
> *:*:*:*::*:22 (-)
> *:*:*:*::*:25 (-)
> *:*:*:*::*:953 (-)
> *:*:*:*::*:993 (-)
> *:*:*:*::*:995 (-)
>
>
>
>
> ##### IPTABLES #####

 

Thank you.
I did this and everything looked right, but I got this error "Failed to reload php-fpm.service: Unit not found." I rebooted the server and all sites seem to work. Problem however is that I still can't enable let's encrypt, the check boxes get emptied just as they did before.

Best regards,
RIkard

 

Thank you. I was about to reinstall certbot when I saw that the new version of ISPconfig (3.1.14p1) was out, I installed it and my problem was solved. I didn't need to manually reinstall certbot. Thanks again!