Are you installing your root server on Windows or Linux? Could you provide some screen shots of the first couple of steps of your installation getting you to this point?
Very early in the installation you have a choice of “Installing an evaluation”, “Installing using a license authorization file”, or “Installing using an existing masthead and key file”.
If you’ve just received a new authorization file from Subscribenet, then you have not yet created a site signing certificate and private key. You’d select the second option to install using a license authorization file, and the installer will prompt you to create a new certificate and password for the private key file. At no point there should you select the certificate or private key file from your first deployment.
I think the message you are seeing implies that either you’ve taken the “Install using an existing masthead file” option, or, when prompted to create a new certificate and PVK you directed the installer to your existing files and it failed to warn you about that.
Or it could be some other condition I’m not aware of, in which case I’d echo Alan’s advice to contact support.