I could very well be mistaken (it happens at least twice a day) but is there not the scope for two frequent flyer numbers in the booking, one being for 'status' (perks) and the other for earning miles/points? I've certainly seen this in the past and have flown on a booking with two frequent flyer numbers so assigned, the first was entered for perks of seat selection and lounge access (using status in one airline's program) while the second was added at the lounge for earning miles/points on the flight itself.