I'm not sure if JAL uses Amadeus, so that might be the reason why the booking reference was not identified. You could try logging into www.checkmytrip.com (a service by Amadeus) and put your AY booking code there. It often gives out other airlines' booking reference's in the booking details.

This has at least worked for me with KL and TK.

With the JL booking code you can log in to JL's Manage My Booking and choose your seat there.