I wish it would retain route selection instead of reverting back to "economical route" every time I load the game.
But that's for the suggestion thread...
I had the same problem. To solve it: Go to this file location: C:\Users\{username}l\AppData\Local\Frontier Developments\Elite Dangerous\Options\Player And simply rename your Custom.Misc file. Once you restart you should find that the map remembers your settings again...