If this happens right when starting a new game, when you haven’t set up any harvest / mining / building orders yet, something else must be messing with the game.
Could you upload your stonehearth.log after letting the game lag for a couple minutes? It’s inside C:\Program Files (x86)\Steam\steamapps\common\Stonehearth.
Did you try any of these workarounds?:
In the second post of that thread there’s a list of applications that can make your game lag like that. Do you have any of them running in the background when the lag happens? It could even be your antivirus.