So you're flying QF-EK X EK-EK? Did you pay for a better seat on the QF flight?

Is there any benefit to checking in online with QF? If not, then don't. If yes then do, but see which seat you get on the EK flight, if they issue the BP.

Codeshare partners usually have specific subsets of seats they can assign and given the extra legroom seats being paid for it might be bugging out on their site. I wouldn't worry too much right now.