The modlist doesn't correctly save, it's always been an issue that comes from the fact that modding was added as an afterthought.

The workaround is quite simple though:
After you've enabled / disabled the mods you want, when you exit the mod menu the game automatically reloads to bring you back to the main menu.
Once on the main menu, entirely exit Banished and relaunch it. That complete stop of the game before you start playing a town forces the game to commit the modlist changes to memory. After that restart you can start a new town and you'll be fine.

(It will also prevent the crashes that happen if you change mods, start a town without doing the restart, and then try to go back to the main menu because you're unhappy with the map. That crash is due to the game getting confused about the modlist)