After changing the core distribution servers objects within the Infrastructure snap-in to use FQDN, one must then update the DistributionTable as well as the 'hierarchy.cfg' file with this change too.
1) DistributionServer table
Close the AS console and then run the following query:
2) CFG file
Edit the "<WHAREHOUSEDIR>\RayVentory\Repository\DeploymentLocations\Common\hierarchy.cfg" file and then save that change:
Distribute the new CFG file to all distribution servers: