If you import an organization from one deployment to another using a SQL backup, the organization keeps it's organization ID. If you import a second organization from a later backup, it still keeps the ID. I suppose that might be by design as it's just a later backup of the same SQL database. How do we import a later backup as a new organization?
This all becomes relevant when performing an upgrade. The deployment manager seems to get lost when performing an organization upgrade if it's working on a duplicate organization ID.