Ok, so.
Just spoken to them again.
What’s becoming clear to me is that you can’t put x2 JAL F-class segments on the same booking, however you try and structure it.
The availability is there - the agent saw it. Then when he searched for another leg, for which availability exists - he then couldn’t see that leg.
It’s like the system automatically blocks them out from seeing the availability if you’ve already added 1 JAL F segment to an itinerary.