Hi there, I believe that I had the same issue with my CX flights booked as part of a QF Award - was not able to book seats on the QF website apart from aisle or window preference.
From memory, the way that I was able to choose our seats was to use
www.checkmytrip.com and open the booking using the QF PNR and surname. Under the CX legs, there was a different PNR listed. I was able to use this other PNR on the CX website under Manage Booking to book our seats for the CX flights.
It did take a bit of fiddling with the booking name on the CX website though - I seem to remember that it worked with just my first name and surname in the end (ie no middle names required).
Hope that helps - sorry I can't be more specific as it was some time ago that I had to do this!