Grrr i am having this trouble too.... used to be no problem adding another FF number after the booking. Given that some bookings (such as booking Avios via QR.COM) automatically use the QR number.

This is not great as I cant use my oneview benefits, even the usually helpful Twitter DMs dont work, and they advise the following (not very helpful)

"we are currently unable to update the membership number to the booking due to recent changes in our procedures. However, you can easily update your membership information at the airport check-in counter. Thank you."