Hi TeleFragger.
Some Altiris previous versions you could to paste the folders with the packages and the altiris were able to identify these packages.
I'm running the same version as you and sometimes I face the same situation. As a "workaround" I setup the new site server in a site where already exists a site server with all the packages replicated.
I only install the Altiris agent and package service in my new server. All packages will be replicated from the other site server that exists in your location. When the all packages be replicated, shut down the new server and also delete it from the Altiris console. When the new server arrives and be installed, the altiris agent will appear in you console. Then, install the package service again and packages replication won't be necessary because you already did that. The agent will only verify each package and show package ready.
I hope this help you.
Regards,