Well, the writing of new data uses the same method as the Map works, saving information to a separate POI file, which is one of the files you listed above.
I'm not sure what would be preventing your game from successfully writing to said file.
Where do you have the game installed to?
Any sorts of anti virus running?
Just kind of stabs in the dark, but maybe we can make sound ground on the problem.
At the very worst, I can explain how to edit the default file for you from out of game.