Originally booked with CX FF number, then subsequently changed before the trip to BA FF number. BA FF number on all the relevant boarding passes; check-in and/or gate agents confirmed that it is indeed the BA FF number rather than the CX FF number. And yet two of the flights still ended up being credited to CX despite the BA FF number being on the boarding pass - so even within the same e-ticket and trip they managed to correctly credit some legs to BA and incorrectly credit one leg to CX.