There is a field on the Contact record in Luminate CRM called Address Standardization Status.  Whenever an address is changed, that field is changed to Standardization Pending and so when the Address Standardization tool runs, it will attempt to standardize any addresses that are marked as such.

To prevent the Address Standardization Tool from changing these manually set addresses, change the Address Standardization Status to Manually Set and the tool will then skip those records.