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.