Acme.sh generated certificate for ISPConfig interface wrongly linked to other domain names

I have scoured every forum post and every guide or option I could try to fix other domains from being link to the main ISPConfig certifcated generated by the force install flag on ispconfig_update.sh. Technically it worked by generating certificates and the Postfix symlinks chosen during the wizard exist but in practice it is not working properly.
The config prior to using 3.1 worked fine by creating websites and alias domains: example-customerdomain.org and mail.example-customerdomain.org although letsencrypt was not working well while now it works automatically. I have disabled SSL and Letsencrypt tick boxes in the ISPConfig interface numerous times, re-enabled them and then restarted services but to no avail. The only certificate that shows up on HTTPS and SSL connections is from example.org not the 'customer' accounts.
All old certifcates were deleted and the only backup ones are from the acme.sh script generated through the ISPConfig interface exist. They are also created in the correct locations under the "ssl" directory a level above "web" as well as ISPConfig ones under the default directory. Any ideas of what I can look for to resolve this issue?

 

I think the main cause could be you migrated from certbot to acme.sh which is not advisable as old config from 3.1 is most probably using certbot. If that is so, you should revert back to certbot.

However, if that is not the case and you are using acme.sh all along, do check what is the hostname fqdn for the server, because ispconfig installer will always use it to create the server SSL certs as there is a possibility that it was not correctly setup causing acme.sh to issue certs for example.com instead.

Just some guesses to help you figure out what was the real cause of your problems.