It sounds like you booked an AA-marketed, AS-operated flight. In this case, AA took your money and issued a ticket, but AS will be the one actually hauling you around.

Seat assignments are owned by the operating carrier. When the ticketing carrier issues a ticket, the seats you selected were seat requests sent along to the operating carrier. AA basically told AS: please take this money in return for transporting John Doe on flight 1234. Oh, and by the way, if seat 9A is available, please reserve it for him.

In most cases, that request is received and respected without any problems. But in the case that the operating carrier (AS in this case) has schedule, equipment, or other operational changes, it may not be able to fulfill the original request for seat assignments. It doesn't bother to tell the ticketing carrier this - that transaction is already complete. This is why your seats never update on AA's site. AA only shows the seats you requested at the time of your reservation. There is no syncing in place for seat assignments to original ticketing carriers.

In short, select your seats for your AS-operated flights on alaskaair.com. The seats assigned to you there will prevail. Anything shown on aa.com is out of date, doesn't matter, and won't be updated. This applies to nearly all tickets where the marketing carrier is different than the operating carrier.