I haven't looked into this for a couple of years at least, one of the updates changed something where my game always defaulted to a custom preset for the galmap filters instead of whatever I left them set to. The most obvious sign of this is that on entering the game the galmap filter for star class is always the one shown, and L, T, Y and Proto-stars are always un-ticked. This is a filter I commonly used to use & having it always there is no biggie although with the 20,000ly route plotter doing all the filtering of scoopable stars for you it's less useful than it used to be.
So I'm looking in C:\Users\myusername\AppData\Local\Frontier Developments\Elite Dangerous\Options\Player
In there I have a file called .misc dated 6th Oct 15 and I can clearly see the filter I just described. The file isn't read only. I also have a Custom.misc with today's date, clearly updated every session.
Finally I have a file called StartPreset.start which only contains the single word Custom, date modified is 18th Jan 16.
So .misc would seem to be the default if no custom is found, then we have a custom setting (ie my last settings) and a flag that says to use the custom one.
The file structure makes sense, but the galmap filter stuff and presumably the route plotting setting is using the old file from 2015 instead of the one from the previous session.
The Player folder is marked read only but none of the files in it are, and the custom.misc is clearly being updated.
I'll take a backup of the folder & try deleting different files to see if the behaviour changes. Any suggestions welcome but what might be useful is to know what others see in this folder.