Did you make your bookings as a Sapphire, or were you already Emerald? Sometimes the system recognizes your status at the time of booking and it stays that way unless you try to change/re-enter your FF number (something I always struggle to do on AA/US bookings!). I'm guessing you have probably tried this already to no avail but I thought I'd throw out a possible reason just in case it helps. Sorry you seem to be having so much trouble!

I'm not surprised this problem is limited to AA/US, however, since they use a completely different reservation system from other OW airlines.