i use virtualmin <> webmin on my server, and i use letsencrypt for my ssl certificat.
its very simple for generate a certificate on new virtualmin version ...but...
Letsencrypt use "urllib" for generate certificat in this folder :
.well-known/acme-challenge
the user-agent "urllib" its in the default list on admintools (htaccess).
for automatic generation of letsencrypt certificate works correctly in the virtualmin panel, remove "urllib" from the list of user-agents to block. ...and then it works!
I took some time to find which was crashing the certificate request.
it might be well to add this information somewhere so that it is read
Thank you
doc_denis, a french user