I've been investigating several different cases where alias server backups fail. One mode of failure appears to be when you move an alias domain from one primary server to another. It appears the move function doesn't create the 'domains/alias' folder for the destination server. After that backups will fail when the '.backup' folder cannot be created in the missing folder.
Creating backup for virtual server fooalias.bar.com ..
.. failed to create temporary backup directory /home/foo/domains/fooalias/.backup : mkdir: cannot create directory `/home/foo/domains/fooalias/.backup': No such file or directory
This can be fixed by simply creating the missing folder, however I guess this is a bug in the move server function?
mkdir -p /home/foo/domains/fooalias
chown foo:foo /home/foo/domains/fooalias