It is possible QF and EK systems don't "talk very well", but I can GUARANTEE you that QF and LAN systems hate each other's guts and do their best to stuff up everything. Try booking a seat (even if WP) on a QF metal, LAN codeshare - absolutely impossible.
Second that. Qantas seems to think the PNR for QF and LAN systems are the same. Despite what they say, it is most definitely not, and there is always a mad scramble for seats at the gate.
On a recent flight with EK on a QF codeshare, the QF seat selection stuck. Being in F may have helped.