Since the game is already updated to 1.3.1, then you should have downloaded the 1.3 tools (which I believe are at the very top of that page).
Did you place
all the contents of the .zip into the correct spot (Which should be C:/Program Files (x86)/Steam/steamapps/common/Amnesia - The Dark Descent/)? That includes the editor and viewer folders.
Have you tried a Steam Integrity Check?
- Right-Click the game in your Steam library
- Click "Properties"
- Navigate to "Local Files" tab
- Click "Verify integrity of game cache"
If there are any properly missing .dlls from the core game, that should fix that.