This is an EXTREMELY annoying feature of the BA system. I have had similar problems in the past. I was never able to get the first number out once it was in, and it took a number of phone calls and faxes to the manager of the local BA Executive Club to get them to transfer release the points so that I could get them credited to another scheme. You should make sure you keep all your boarding passes and tickets until you have the miles in the scheme you want.

Insisting that the check-in agent makes the boarding pass show the FF scheme that you want helps, but it almost certainly won't make the points go there until you go through the faxing/phonig routine.