I have perused this thread from the beginning. You have informed us, @nsarantopoulos, about what you view the problem to be rather than what are the operations that you carried out in Virtualmin and what the outcome of those operations was.
Let me tell you what I do to get a SSL certificate.
I create a virtual server - the SSL website check box is enabled by default.
In Virtualmin → Server Configuration → SSL certificates, I use the Let’s Encrypt tab to request a certificate.
If the request is successful, the certificate from Let’s Encrypt is applied and the website shows the lock symbol. Yay! Mission accomplished. If unsuccessful, I.am left with the self signed certificate that Virtualmin had assigned to the virtual server.
That’s how it works. Now tell us what exactly you have been doing to see just the self signed certificate.
It’s great it worked for you but as @calport said, it would be useful to explain what operations you undertook for the problem to arise. That would be really helpful for newbies like me if I had the same problem as you.
Thanks.