Did your son hold the Alaska credit card, or did you and booked the trip for him? I can image the system is unable to pick up the second case for the free bag rule (or the free bag doesn't apply in that case, not sure what the exact rules are). Also likely an agent cannot trace where the wallet funds originally came from.

On the other hand, if your son did indeed hold the card, it should not matter how the ticket was paid for.

https://www.flyertalk.com/forum/alas...gift-cert.html

BTW: if you are sure the bag should have been free, just raise a case with customer service and ask for a refund.