I have been to every single location for that achievement, some of them several times over, but there are five locations that will NOT update: Crystal Nook, Hidden Grove, Reishi Cliffs, Zelda's Perch, and Higher Thicket. There are clicky items near some of these locations which I have found but cannot click to get the quests yet as I have not yet done the Adventure sig line. One of these locations was difficult to find, but I found each and every one of them, yet they did not update. In fact, the ONLY update I got when I began focusing on the locations I had yet to find was the Stormsview Pond, which is the LAST update I got towards this achievement.
It wasn't until I finished the Adventure Sig line that I could get credit for locating those places. Clicking on the objects gives a quest.
You can't get the clicky quests until you finish the sig line, either, even if you manage to scramble up to wherever the clicky items are.