I have the steam version of Machine for Pigs and the saves don't work correctly. It seems the game is picking random saves to load. My /home/xxx/.frictionalgames/Amnesia/Pig/xxx/ directory contains some files and other start with AutoSave_blah.sav and others with autosave_blash.sav.
I've disabled steam sync but the problem remains. With the steam sync disabled I've also deleted some of the save files and kept what I wanted but magically the saves re-appear.
Also another user is experiencing the same:
http://steamcommunity.com/app/239200/dis...451901788/