If your bank relationship is in your template (on both the gift mapping as well as the bank relationship mapping), but your imported gifts do not have bank relationships linked, you should also check to ensure that your gifts were mapped to include the pay method of "Direct Debit" as this is necessary in the Raiser's Edge to link a Bank Relationship to a Gift record.
Below, you can see the Bank is unavailable in Batch for the Cash gifts, but it is mapped correctly for the Direct Debit gifts.
