You need to ask AA to remove your Alaska frequent flyer number and enter it manually (this sounds like a pain).

FFAS1234567/AA-1.1 is the manual entry. If they don't do it this exact way, it will say emerald status, but there is a secondary system on top of Sabre that won't recognize it.

This affects 1000% of all travel agent and corporate bookings because the generic way to enter your frequent flyer number into Sabre is FFAS1234567-1.1 (FF = entry AS = Alaska 1234567 = your MP # AA = link to American Airlines 1.1 = passenger 1 of 1 on the reservation). If its done THIS way, you'll still get Main Cabin Extra, but you won't get baggage waivers or upgrades. Boarding Pass will reflect Group 4. Get it fixed, and you should be free bags, UPP3 on the upgrade list, and Group 2.