I logged into QR website today and my seat selection that I made via Japan Airline is still there, are you sure you made the seat selection on Japan Airline website? You can only access your booking via Japan Airline if your itinerary has at least one segment with JL, as otherwise you can't get past the login page.

Also, you need to confirm your seat once next to the seat selection you made per flight and one more time at the end with the confirm button at the bottom of the page, did you do both? I got caught out at first and didn't realise I had to double confirm my seat selection on the page.