For all domains with MySQL databases the backup fails for this reason:
Dumping MySQL database freshit …
… dump failed! Warning: Using a password on the command line interface can be insecure.
Server version: 5.6.5-m8 MySQL Community Server (GPL) - CentOS
The backup file is ok, it contains all databases but we receive a failure message every time by email.
It’s too late to post, but I had the same issue yesterday and found out that it was because I saved root password in the file /root/.my.cnf
I had to delete it.
Its a warning in 5.6.
The official line is that you shouldn’t call mysql with passwords on the command line and should use the credentials file.
Obviously Virtualmin does things in a certain way, the work around is to say ignore errors and continue and it works fine, it’ll say failed but everything including databases is there.