They appear as having been taken by someone else because Amadeus probably still has record of the old seat selection (albeit as unconfirmed).
The problem is when you make a change on EK's site (Mercator), it tells Amadeus about the new seats, but Amadeus ignores Mercator if the Amadeus record already has seats against that flight (irrespective of the status of the seat assignments Amadeus has got).
If you wipe out the seat selection in Amadeus first so that there is no seat selection showing in Amadeus, then set a seat assignment using the EK site it flows through over to Amadeus correctly. That seat assignment then needs to be confirmed (HK'd) on the Amadeus end by QF.
Before you hold QF to this broken functionality, it's Amadeus at fault. It not only happens with flights operated by EK, but also AA, AS, WS, and just about any non-Amadeus carrier.