If the batch template matches constituents based on the global [data entry] settings try the following:

1) In the batch template settings, uncheck the "Use global settings" box so that the batch uses its own constituent matching settings and click save.
2) Open the batch template settings again then check the "Use global settings" box so that the batch uses the criteria from the global data entry settings and click save.

This has been known to fix matching issues in the Membership Dues Batch.