It may just take time, but last time this happened to me BA had managed to put my BAEC# in the reservation for the BA flights - the credit didn't show up on AA because I had already had the Avios from BA. I had to call BA and ask them to uncredit me those Avios, and once that was done I resubmitted the missing miles info to AA and they credited right away. Could this be happening to you here?