I need help

[Oscar House]

This happens with a lot of games that have their own launchers. Steam only marks you as in-game when the Amnesia launcher is running, so when you start the game through Steam, here's what happens:
1. Steam starts Amnesia launcher.
2. You start the game through the launcher.
3. The launcher closes itself and starts the game.
Since the launcher is now closed, Steam no longer thinks you're in-game.

If you want Steam to track the time you spend playing Amnesia, start the game, alt-tab out of the game and start the Amnesia launcher again.