In Virtualmin -> Server Configuration -> Clone Virtual Server window the following notice is given:
Warning - any web applications in the cloned virtual server will continue to use databases in the original virtual server until their configuration is manually changed.
I wonder is there any particular reason why any new cloned server can't use new database and has to use database of original server? I probably wouldn't happen on this matter for a long time if a user on my server didn't actually cloned couple of servers and as a result only last cloned server was working while original one and first clone could not connect to DB. Because their databases had no users at all. Though they, no doubt, had users with correct permissions before cloning.