If it is still the same as in WoD, then you'll get the upgrade of the mission only after the weekly reset, so if you got the mission in the same reset as when you got your eglectible kill then you won't get the upgraded mission just yet and have to wait until you get one after the reset.
Edit, also, generally you start at a higher cache than LFR if you've done non-LFR raiding in the previous tier.