The 1.106 patch fixed this issue for me.
Thanks for saying that, it made me realize GOG 2.0 hadn't updated the game, and checking for updates didn't do anything. Yay for GOG offering offline installers for patches.
It is fixed for me as well now, starting to get achievements - only a bit of a bummer that they don't retroactively unlock after so much playtime.
Edit: Rude of me - thanks for fixing it though, Atom Team! :D