It's possible that there are 2 BA PNRs in the booking due to the AA flights in the middle (usually due to the fact that BA are in Amadeus and AA on Sabre GDS). Have seen this a few times with bookings made on AA.com with a mix of BA/AA, guess it may also be possible for a booking made on BA.com. Calling BA should allow you to get the 2nd PNR if this is the issue, when it has happened to me on a booking made on AA.com, I had to call AA to get the extra PNR.