This hasn't been an issue until the last couple days, but I played for a while yesterday and today, and when I exited the game my progress through the map hadn't been saved. I activated a couple of waypoints that weren't active after exiting the game and re-entering. One of those I even made it a point to actually use the waypoint to return to town prior to exiting the game. There's also one point in the middle of 2 waypoints that still shows as being unexplored on my map, even though I went through that area to get from one waypoint to the next.