Thanks for trying to help my. Hopefully I can give you more information:
I have 2 Plesk Panel Servers this issue persists on both machines... Maybe I have made an mistake installing the certificate, but I did everything by the book. Uploaded my certificate under Certificate and Uploaded the intermediate CA and root CA under the second file upload.
After that I selected this certificate and used the secure panel function. At the first try this issued a "Template_Exception: Syntax error....." error. But only on one of the two servers. At the second try everything worked normally and I think this step produced the httpd.pem and rootchain.pem file under /opt/psa/admin/conf/.
Since pop3,imap,smtp do not use the panel certificate not even after you set a certificate corresponding to an IP Address under Tools & Resources->IP Addresses. (why should you do this anyway?)
I edited the config files "pop3d-ssl","imapd-ssl" under /etc/courier-imap/ and set the TLS_CERTFILE pointing to the httpd.pem and since this file is only (on my two servers) contains the private key and the certificate the TLS_TRUSTCERTS variable to the rootchain.pem file.
Same with postfix in the /etc/postfix/main.cf file with the "smtpd_tls_cert_file" and the "smtpd_tls_CAfile" variables.
With these settings I could verify with openssl that the SSL chain is working correctly with pop, imap and smtp.
Only the panel SSL is failing as it obviously only uses the httpd.pem file.
I'm curious why mine only contains my PK and Cert and not the intermediate CAs when yours contains everything...
Maybe the panel failed combining these two files together?
I grep'd the server for "rootchain.pem" and the file seems to be referenced in some files...a
By duplicates I meant if it would be a problem for courier, postfix if they load the httpd.pem file containing everything and then the rootchain.pem which also contains the certificate CAs.
Edit:
Another thing I just noticed:
When I try to access my panel under
http://domain.tld:8443 it get the message "400 Bad Request The plain HTTP request was sent to HTTPS port" and it says "nginx" at the bottom, so I'm using it after all but not that I knew of....