Gift Certificates part payment not showing on invoice when using Bank Transfer mod

I have had 2 customers use a gift certificate as part payment on their orders and the invoice doesn't show a balance of what they still owe or that anything has come off their invoice at all. They have chosen bank deposit as the payment option.
This makes it hard unless I know they had a gift voucher I am looking for a payment off the full amount not an amount less the gift certificate as the invoice isnt showing that the payment using the gift certificate was used or minus ed from the total amount owed.

Maybe I am missing something but any help would be appreciated.

1. What version of Zen Cart?

2. If you do a trial payment using one of the built-in payment modules, does it work any differently?

Normally the amount of Gift Certificate redeemed will become another subtotal entry which is subtracted from the amount owing, and then the remaining balance is processed by the selected payment module.

It's hard to know whether the payment module you've used was designed to use the remaining balance for its records or just the merchandise total. You may have to do some custom coding to get it to use the right information, modeling it after one of the built-in modules.