Eu encontrei o problema, e é um pouco trivial :) De o manual (emph. Mine)
Depending on your backup strategy, you may not want Dirvish to cross filesystem boundaries when performing backups. By default, the parameters passed to rsync do not instruct it to remain within a single mount point on the target filesystem. If you want to have a vault for each filesystem being backed up, you will want to enabled the boolean option xdev. If not specified, the default action is to descend into all filesystems that may exist under the specified target.
Agora, por algum motivo, um dos cofres tinha um arquivo de configuração que substitui esse padrão:
xdev: true
Remover esse sinalizador deve corrigir meus problemas.