You should be able to add it during check-in, but it is odd.

You could email the Thai contact centre, and ensure the name order and spelling is exactly as in your ff program.

I recall once having trouble entering my SQ number into TG’s system, but that 15 years ago and IT systems have moved on. Sometimes staff screwup correctly entering the full code. I think it needs to be something like XXFFFFFF where XX is the carrier and FFFFFFF is the frequent flyer number. Probably depends on the backend system.