Sorry for the waiting. Finally have some time for Factorio modding.
Thanks for reporting.
I was not aware that can be optional, and was not expecting mod settings being changed by script.
Just released 0.17.16 / 0.18.8 / 1.0.2 / 1.1.1, which (hopefully) fixed the problem.
PS1: BTW, your "Show labels" hotkey/option is global, which means it will also affect all other players in a multiplayer game. Right? From a first glance (without actually testing), I thought its nature would be similar to "Alt-mode" hotkey and display, which is per-user basis.
PS2: Some of my earlier-written mods have similar syntax in runtime_mod_setting_changed() calls. Seems I will also need to update/fix them in a few days...