Still broken
I just spent over 30 minutes (mostly on hold) with AA and got the same explanation that I couldn't select preferred seats because the ticket was booked with an outside agency (which it was--the online booking tool for my work). I kindly insisted that the booking method employed didn't change my status and its benefits. Eventually the agent spoke to her supervisor and between the two of them decided to override the charges manually to give me the seats I wanted. The AA helpdesk was not available, apparently.
I also called the AS partner desk while on hold with AA. The agent told me she had no idea why I couldn't select the preferred seats. Since I didn't have an AS confirmation code for her to look up she simply told me there was nothing she could do. I asked her if she knew why the partnership was not functioning as advertised and she suggested I call AS customer care tomorrow (too late tonight). She did not offer to contact AA on my behalf.