When relationships are created in the application, a Globally Unique Identifier is created to identify the relationship pair. This ID is not being created when the relationship is generated via Constituent Update Batch.
Download and install the latest patch which contains all fixes from previous patches. If you are running an older version, download and install the latest version and then the patch.
Steps to Duplicate
Manually add a new spouse relationship to a constituent via the Relationships tab or Add Spouse tack on a constituent record
Add a new spouse relationship via Constituent Update Batch including the following fields: