From what I understand you'll have to sort this out with your FFP rather than the airline. You have a claim against your FFP, your FFP has a claim against the airline. With your boarding pass, you have proof that the airline acknowledged your FF#. If they credited to another program, this is their problem to figure out. As long as the details are on the BP, your FFP should be able to work it out eventually.
QR will most likely give them a hard time so don't be surprised if it will take some time and effort. It will probably be solved through some default rules when QR won't react within contractual time limits.