When you are setting up ID stores for the default tenant in vCAC (vsphere.local), you are given the option to use Active Director or Native Active Directory as the Type. With the vCAC 6.0 GA build, there is a known issue when attempting to use the Native AD option (which is preferable option) with the vCenter SSO.
If the vCenter SSO is already configured with Native AD, you will not be able to configure any additional ID Stores for the default tenant and the existing one will not work. In mean time, you should be able to use the standard Active Directory option for newly created tenants.
The issues will be resolved in SP1 due out next month. This is only applicable when using the vCenter 5.50b SSO instead of the Identity VA.