Sorry to everyone who was impacted by that. Once you take the latest patch and run the game, you'll earn all of your Steam achievements--no need to go back or replay anything.
Also, hello to all of our new players coming from the Humble monthly! We're *humbled* (hehehe) by all your positive reviews and comments--usually going into a big bundle like this means a lot more thumbs down. =)
Thank you all for playing and sharing!