It seems to only happen if settings are changed and the game immediately saved (without resuming for a tick to let the mod process the changes). I'm guessing this is because the mod installs a handler to react to those settings, which can only happen when the game is unpaused. If the handler never gets run (because the game doesn't unpause), I'm thinking Factorio doesn't save the changes.
Tinkering with it though. Can you try the above? (Change a setting, unpause just a tick, then save/reload, etc.)?