I think the guess is just the JAL agent simply was confused and didn't realize they could only see standard availability. With a lot of airlines standard awards are implemented as a standard booking class that can show up in GDS, while the dynamic awards are...something else altogether. Were you contacting the main Japan line or one of their global offices, and did you use the specific department for award bookings? (IIRC I recall a separate call menu item for that). I've seen signs that a lot of their global offices operate more like travel agencies with more privileges when I've had to call in to make changes, so it's possible the IT for the regional offices just doesn't have that level of visibility. I vaguely recall warnings to only call the central office for award related questions, but I could be getting them mixed up with ANA.

Anyway if you are really intent on booking at that award price, you could try getting a hold of the main Japan office in English. They may have more information.