Where did my gift card balance go?

Once redeemed you shouldn't need the card again. If you can't see where it went (an account's purchase history shows how items are paid for, and iCloud storage upgrade payments would have used it) see if iTunes Support can help : http://www.apple.com/support/itunes/ww (click on your country's flag, the country where you live, and which is therefore the country on the account ; click on Get Support down the page)

The only ways for a balance to go from an account is to have spent it, or to have contacted iTunes Support and asked them to remove it. You haven't bought anything on the account, neither  iCloud storage nor purchases, and only have the one account ?