Issue:
When applying a gift certificate to an order, Magento doesn't currently see that as a payment on the order. It's applied as more of a discount as far as order totals are concerned. Since most OMS / ERP applications look at gift certificates as a payment instrument this can cause unneeded customization. See the attached screenshot for more information.
Solution:
Apply the gift certificate as a payment instrument and list it as a part of the Total Paid on an order.
Example