Same thing's happening with me; I have most of the available DLC installed, and it is ticked on the launcher but says it is inactive in the Content tab in game.
I also have my own mod, Orbis Antiquus, ticked in the launcher, and it has worked fine until I tried earlier today to publish it on the Steam Workshop. Since then it says it is active but the game acts as if it isn't there. This is also the point at which the DLC stopped working too.
I'm running 1.3.2 d2a0.