I know it is frustrating but you can avoid a lot of hassle by paying attention to how the system works.
For example, you may have noticed that when you pay for a ticket online, it goes to "Ticket Pending"; sometime later, that becomes "Ticketed". This means that some processing is done after a payment/order is accepted, to make sure all is well.
When you use a gift card, the system immediately verifies that the card is valid one, but it does not check the available balance. That is done a little bit later.
This is why one of the constant refrains at FT is not to relax until you get a ticket number. Without that, record locator etc don't mean anything. This is true regardless of the mode of payment.