This is seriously going to put me off of Dishonored. My second playthrough is a non-lethal run, and I just finished it. Every single checkbox is no-one killed, and I didn't do any side quests besides that granny duel, and I helped Slackjaw out. Alright, so why didn't I get my non-lethal achievement? I'm done with this game until this gets fixed, because I don't want to wipe my progress.

Same here. Every mission report that I have has "Didn't Kill Anyone" checkmarked for my own non-lethal run. I didn't get "Ghost" either even though "Ghost" is also checkmarked for all of my missions.

Does anybody know if killing* the assassins at the very beginning affect this achievement? I hope not...

*Not sure if I actually killed them, they did the vanish into feathers/whatever thing.

Did you
That may jank Clean Hands.

You should edit post about the beginning. This'll probably be moved anyway, but
To use spoiler tags, do this only without spaces.

[ spoiler ]This is a spoiler[ /spoiler ]

So it'll look like:

Some think it does. I just did the defense thing and didn't fight back in case that was true when I started

I've also , but some have gone through the game and completed all the sides and alternates, and still got the achievement, though.

It might be that if you knocked someone unconscious and you moved them to an area infested with rats the rats ate them. Im not sure if it shows up as a kill but i know it counts as one.

Helping Slackjaw out is probably where you went wrong. In my playthrough I pick pocketed the key, hid under the stairs until Granny Rags was far away then bolted for the door. I left Slackjaw but it didn't count as a kill, and I didn't get an alert for pissing off Granny Rags.