https not show LE ssl certificates

Hello, I have a fresh install on VPS. All updated to the last version. Then adding ssl to vhost - LE confirm that all pass (i can see cert has been created) however if I open its still show me warning that website is not using ssl - that is wrong with that? that i need to enable, setup?
Also webmin itself also dont run under ssl (its opened ok by https://) if I try to save Webmin>Webmin Configuration>SSL Encryption its drop me error:
“Failed to save SSL options : The SSL private key file /etc/webmin/letsencrypt-key.pem does not exist or does not contain a PEM format key”
but key is there, and LE confirm that its valid certificate. Confusing.

Big thanks to Peter Knowles who help me out with that problem, even better he show me a proper way to do an installation and now all stuff is working as it should!

Could you please post how you solved that problem so that it can help me and other users? Thanks!

EDIT Actually this is a bug of Webmin.