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If the cardinality of the commerce_customer_profile is not 1 then the EntityMetadataWrapper is not EnityDrupalWrapper therefore we need to interate over the metadata and update any of the the uids of any referenced customer profiles.
Line 769 of commerce_cart.module converts an order over when logging in. It makes several presumptions about the Entity Metadata Wrapper and therefore if the cardinality of the field on the order is not 1 the user can not login.