It's possible that, in the puzzle where [spoiler]you must prove that the machine is not perfect[/spoiler] that there is an untenable assumption.
Consider: [spoiler]the machine says /yes/ to the statement "You wonder if that's a clue?". The machine is agreeing that -you, the player, are wondering if it's a clue-. That does NOT imply that the machine thinks smugness is a clue, rendering one of the assumptions you must make untenable.[/spoiler]
The first time I played, closed the game, and came back later - I thought I'd lost all my progress because I accidentally hit the 'r' key. So I redid everything, got even further the second time.
This time when I quit, I hit esc to go back to the main menu and then hit x, just to check - and it brought me back to where I was. So I thought it'd be okay to close the tab and come back later.
NOPE. All my progress in this game has been lost TWICE. What gives?