I was playing on my work computer and am now at home so I can't attempt to retrieve the .sav file until tomorrow (if I can even figure out how to do so), but the save was made while in Stage One, can't remember off the top of my head if I was on the puzzle-select screen or already in one of the top two puzzles on the Assembly Step 1 board.
I'll try replaying up to that same point on my home PC and see if the issue I encountered happens there too.
UPDATE:
Got up to the intermission board after clearing all of Stage One at home, made a save on that board and restoring that worked fine, then an additional separate save made after selecting one of the Stage Two puzzles also worked fine, so I'm not sure what happened earlier either.