Can't help with your question but I've had a similar problem when segment 3 of a 4 segment same day return on BA didn't credit to my AAdvantage account. No end of me arguing that the only possible way I could have flown legs 1 and 2 with 4 was by being on leg 3 convinced BA that the flight miles should be credited.

With that sort of attitude, I'm not confident I'll get what I'm entitled to but any suggestions would be appreciated.