Check to make sure you have done the laboratory in the south east. The quest giver doesn't show up unless you follow the silly little light that randomly appears when you get near by. That's the 5th light!
there was definitely no way to tell ahead of time you would lose the achievement by making a not-necessarily-bad choice.
--Myrron
yeah the quest doesnt give any kind of warning that you wont get the light if you let the tree live. silly design decision