Im actually having this same problem. My mods worked yesterday morning when I played, came back after work, and nothing. Ive done all that Joey has done like uninstall then reinstall to another drive but still nothing (both game and mod pack). Steam says all is ok, and yes, I installed it to the most current game build folder. Looked at what draco said and all looks fine with the current version, its 0.8.9.1 now tho. No clue whats happened :(
Edit: So I installed some mods manually and they still dont work with the steam version... as I expected, theres something wrong within the game/folder itself