The game prefers to use the unzipped version of stonehearth if it sees both an smod and a plain folder. If you have the game unzipped, when steam updates it will only download the new stonehearth.smod and leave your unzipped version alone. So the stonehearth.smod is newer and the unzipped folder is still the old version. Then, when the game goes to look for the stonehearth mod, it will see that an unzipped version exists and prefer that one. Since the unzipped version is the old version, you will not be running on the latest version of the game.
Hopefully that makes sense. XD