It's also important to point out that JAL doesn't allow seat selection on some of the cheaper fare codes (including for their own elites). Often times the JAL website (which I have to say is horrid from a customer standpoint, most particularly on codeshares), won't even let you view the seat map.

This thread is particularly helpful Selecting seats on JAL when booked as AA codeshare

My first time with JAL was on one of these BA coded JAL flights, and indeed, as a Silver, I could not select seats until checkin (which happens to be T-72hrs for JAL).

Try booking the straight JAL-prime flights (in an eligible fare class) or take the BA services to TOK. I suspect you won't have an issue.