On a game started and played completely under 1.41, I won as the Yor and defeated the Iconians while doing so. Yet the "Exterminate" achievement, which is for destroying the Iconians while playing as Yor (i.e. what I did) was not awarded. During the course of the game the "I Assume You Were Talking Back" and "World Without Flesh" achievements were awarded, so it wasn't a problem with all achievements.
One funny thing, I remember seeing the achievement flash in the upper left corner of the game when the Iconians were defeated, but when I look at my summary in Steam it's not there.