Your DarqUI settings are saved as custom mapping files. For Live servers the settings are saved in the DarqUI_v3\POI subfolder; for Origins servers they are saved in DarqUI_v3\POI_Origins. If your UI files are configured for the wrong server type, it can appear as though nothing is getting saved.
On the Settings page of the DarqUI utility, down near the bottom, choose the correct server type from the dropdown. Click the Reset files button even if the dropdown already showed the correct server type. Restart the game and your in-game settings should be saved between game sessions.
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