Hmm.. this seems like indeed a structural issue with some (mysterious) changes that KLM/AF IT did to their system. I am having exactly the same issues...the original FFP number that you have inputted seem to be hard coded and even changing at check-in and it showing up on the BP, the miles still goes to the original FFP.
I've written a couple of times to KLM/FB and they are denying any changes - although it has happened to me already 4x now - I've not been able to get a clear answer on this.
It seem to happen somewhere end of last year.. as before November, I did not have this issue.

I would suggest that you write to KLM (via Customer Service and the complain form).

Although coming back to your issue, you will have to write to Garuda to ask them to remove those miles and resubmit a retro claim to Alaska.

Cheers!