This happened to me about 2 weeks back on SFO-SYD, booked on the AA codeshare. Connecting on to QF op/marketed SYD-AKL which I could select a seat for, but not SFO-SYD. Both QF and AA couldn't do anything either, though QF said they "left a note for our check-in team advising your seat preferences". Not sure if that led to anything but eventually at T-80 the seat map showed up on QF's manage my booking and got myself a seat.