Yes, lots of people (including myself) have had the same experience going back a long time in the Oneworld Award thread.
I believe it comes down to a lack of training - don't understand the details of their system but others have mentioned it requires the CSR to look for the JAL availability in a different system. They either forget or don't know to do this.
Just HUCA until you find someone who can see the availability.
Edit: When you do find a staff member that knows how to book it, can you please ask them what exactly they need to do and post it back here for the benefit of all of us.