I don't think I've ever came across this issue. Do you have an active quest in that poi and it's bringing up the quest marker or is it just a dead spot that you can't build in?
dead spot you cant build in , the rally marker is always there just invisable you cant delte it or see it if you happen to need to a put a block there you cant but in game you cant tell whats going on if you go into the poi editor you will see the rally marker in that spot
Shift-left click on any block in creative mode removes it. . . . or maybe it's shift-right click. Dammit, now i am going to have to open the prefab editor and confirm.