Hi Peter, to clarify
VSC is context sensitive to the datacenter selection. For example you have 3 datacenters A,B,C.
If you were to select datacenter A in vCenter and then go to the VSC Overview panel, you would only see controllers that are associated(have storage mapped to) with ESX hosts in datacenter A. Similar behavior on selecting B and C.
If A , B and C are datacenters under a common folder and if you were to select that folder in vCenter and then go to the VSC Overview panel you would see all the controllers associated with ESX Hosts in datacenters A,B and C.
When you mentioned that the "controller was added but its was to the wrong datacenter" , it's most likely because the controller has storage mapped to hosts in that "wrong datacenter" and that's why it showed up there. Can you double check to make sure that the added controller has no storage mapped to any ESX hosts in the "wrong datacenter"