When vCloud is first installed, not all users are aware that System Name will be used elsewhere ... like in the root folder name in vCenter.
I did test this briefly ... but there is no immediately obvious workaround. If vCloud fails to find the folder of the correct name (not MoRef like group-v##), it will create a new folder with the correct name and continue to use this. This logic only seems to apply to the Root folder. The subfolders, for an organization or OvDC, seem to be referenced by MoRef ... not location when it comes to finding them in vCenter.