Neither do I but I’ll throw out some ideas…
Is this the server’s hostname and is there an A record for it? If you are hosting your own DNS Virtualmin takes care of essential A records when you create a virtualhost, but I don’t think Virtualmin takes a server hostname into account. If there’s a missing A record for this name add it manually to the same zone for the other names.
Do you mean there’s no IPv6 at all? or IPv6 is enabled for the server but you choose not to use it? If IPv6 is lurking somewhere in the network LE will find it and expect to find AAAA records. Or IPv6 doesn’t exist but there’s an entry for ::1 in /etc/hosts. If any of this rings a bell you’ll want to make certain IPv6 is thoroughly disabled before going without AAAA records.
Here’s a suggestion that may help with that:
It’s hard to say why http validation fails. Sometimes LE is unable to create .well-known/acme-challenge. Other times there’s redirection occuring in a virtualhost config or http header in an .htaccess file that gets in LE’s way. When http validation fails LE moves on to DNS validation, so I find that it’s easier to correct DNS one time rather than modify a virtualhost every time LE needs to run.