TL;DR
When the user changes startup mod settings as part of a new game, stop throwing away their other game settings on restart.What ?
To reproduce, simply install some mods with startup settings. Go to start a new game. Make some changes for the settings in front of you, like setting all resources to 600%. Click the mod settings button and change startup settings. Restart the game. Now when you go to start a new game, you have to make the changes all over again; the game does not simply take you to starting a new game with the desired settings.I suggest that the startup mod settings should only take effect when the player clicks Play, and the game should then restart, immediately launching a new game with the desired mod settings and the resource/terrain/etc settings. In fact, it would be better if Mod Settings was just one of the tabs, rather than a separate window as now, which would make browsing all startup settings easier.