Just to be sure, did you check the corpse after killing the floating eye to get the KI that you need to give to Aethelmaer? If I remember right, the icon for the KI is a lily for corpses.
http://ffxiv.gamerescape.com/wiki/Power_of_Deduction

Used to run into this a lot in XI--people thought they were done when they won the fight, but needed to check the pop spot again for a KI or cut scene to actually continue to the next leg.