Seems pretty consistent. 4 out of 4 times I went in there, the world reset. Twice with every waypoint and location discovered, once with most of them, and once with only a few. Just to see if discovering a specific place had anything to do with it.
Update: I discovered waypoints will similarly do a world reset, just a lite one. Time of day becomes morning, even if it had just turned dusk, and harvested plants and iron deposits come back. (This also breaks pregnancies .__. )
Since the dungeon door resets everything not directly tied to you (inventory, etc.), even making the initial help (H) screen pop up again, my theory is that it's simply set to load the wrong world state.