When using the backup/restore functionality on a domain by domain basis, I have some domains missing their mysql databases. The default DB that is created when the domain is created is backed up but additional DBs made under that virtual domain are not showing up in the .backup folder of that virtual domain.
Well, I just verified that all the databases (even the extra ones) are being backed up on my system, and they appear to be.
So, what I’d do is perform the backup manually – from the Virtualmin interface – and look the output over when it finishes to make sure you don’t see any errors, or otherwise any references to the databases you aren’t seeing backups for.
If that doesn’t help, I’d file a bug report – all the database should definitely be backed up, and if they aren’t, we’ll need to track down why that is the case.
-Eric