Thanks for all the details. It makes it much easier to debug
This really looks like the bug from 0.4.0 and 0.4.1, where achievements aren't saved properly. It is possible to play the game from start to finish, but as soon as the game is saved (or, rather, when you load a save game) all the achievements are gone. And since some of them are required for future events, you are most probably stuck.
This is fixed with 0.4.2, but the fix is not compatible with save games from 0.4.1.
Sadly, the solution is to start a new game and make sure it is version 0.4.2.