On both space and ground maps, settings are reverted to default with no interaction from the player. Attempting to correct settings to use preference appears to be saved when checked immediately, but reverts to default after some time has passed, or with each map change.
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Opening the "options" menu resets both the ground and space "controls" tab to its default settings.
So merely opening the options undoes any changes you do to your control settings.
As far as I can tell, the only temporary solution around this issue is to set your desired control settings, and never open the options menu again until this gets fixed (as re-opening it triggers the reset).
That might work, but since a reset triggers as well on map changes or just at random, it wouldn't do any good.