I also have the same issue, except it is with 1099 contractor payments. When we pay our contractors, it shows up as a payment and a deposit (which it should not be).
This transaction is not from the bank register but appears to have been created because of the direct deposit payment. When I try to delete the deposit transaction, I am given the prompt, "You cannot delete a direct deposit transaction. If we haven’t processed this payment yet, you can void the transaction and we won’t send your payment."
