I get that message too, but (as long as you didn't choose exit or bulkhead) if you log out of MMB and then back in, normally the seats I selected are then confirmed. Not sure why it happens that way, but has been like that for me ever since QR joined oneworld.

However my bookings are made through a travel agent so not sure if that affects the MMB section I see (it seems to redirect to Amadeus page but branded as QR - not sure if that's the same for direct bookings as well).