At the moment, our new gift card system does not behave the same way as our previous gift certificates. Before, you could just check out and the GCs would be applied automatically. This time, however, you need to enter the actual gift card code (you can see some of them in the checkout page). See our KB article here for more on this subject.
If you applied a gift card with your order but somehow got charged the full amount, this is probably some kind of checkout error and is very likely our fault. (Well, the fault of the series of tubes and electrons between us.) Please submit a Help ticket - don't forget to include your Order number! -and we'll make it right.