Let's suppose that loading a machine with a different set of softwares actually did "create" a new machine.
In that case, each new implementation would be the user's creation. That's right - it's the end user's unique creation, not that of some programmer halfway around the world who coded the individual program.
Or, if not the end user (in a corporate setting) then it would be the creation of the corporation's IT department. Copyrightable and patentable, I would guess. Set the machine up to your very precise specifications, register your creation, and NO ONE can use that same setup unless they license it from you!
Or, we could all fall back twenty and punt, with the admission that this "new machine" business is absurd.