Justine overwrote user_settings.cfg

[Your Computer]

I guess Justine overwrites the config on purpose, doesn't it? ...to prevent you from cheating with things like quicksaving.

I believe the inability to save your progress is built into Justine. If you look at the configuration files for Justine, you'll see that it actually uses TDD's default_user_settings.cfg which allows the user to save their progress. Yet, in Justine you cannot save your progress.