Ambassador: Japan Airlines
Join Date: Mar 2008
Location: LAX
Programs: JAL Mileage Bank, JMB Diamond, oneworld Emerald, Bonvoy Platinum
Posts: 16,400
I got similar problem when the check-in system has a mismatch with the reservation system. They had an equipment change few days before departure and forgot to update their check-in system. F wasn't originally provided before the change and therefore they kept saying my F ticket was invalid when I tried to check in. Not sure if that's your case though...
Make sure you go to the airport extra early. It took them forever to check me in as they couldn't locate my record at check-in counter either.