In both 6.0 and 6.1 admin guide there is this statement listed before the Hardware Requirements and Supported SharePoint Servers. I believe you are running into issues because you can only backup 1 system per farm.
"VDP supports the backup and restore of Microsoft SharePoint Servers. Only one SharePoint Server system per farm is currently supported. NOTE Restoring only the SharePoint Server Configuration or Administrator’s database can corrupt the SharePoint Server application. Therefore, if you are not restoring only content databases, you must restore the entire backup."