You may already know this but…
JAL use Amadeus for International flights and their own system for domestic flights. So since this is an international flight, your BA PNR is the same for JAL.

Two things to check:
1. Make sure you’re on the Manage Booking page for JAL international.

2. On some of the JAL pages they want a 3-digit flight number not a 2-digit. i.e. 048 instead of 48.

Don’t ask me why, but hopefully this helps.