When restoring from a backup with a different datadir configured in my.cnf:
[mysqld] ... datadir = /mnt/RAID
Virtualmin restore does not change permissions on the correct datadir, it tries (and fails, for me) to apply those permissions to /var/lib/mysql/. I temporarily solved this problem with a symbolic link between /var/lib/mysql and /mnt/RAID on this system. If this had been an emergency situation, the time spent troubleshooting this issue could have been catastrophic.