Did your "new" boarding pass show 1A or 25F?
I'd check your credit card account to be sure you have a record of your original purchase and to see if you get charged for an upgrade.
If you get charged for an upgrade another pasth is a dispute with the Credit Card company.
I've also found you get a better response to such issues on twitter than over the phone.
BTW I think the call center is in the Philippines.