Answer by Varaughe

The idea is like that, normally timeScale defaults to 1 in "Edit->Project Settings->Time", but if in your code at some moment you change timeScale to 0(e.g. when you emulate game pause) then that value will change to 0 in project settings, and if you have the bad inspiration to "Save Project" in Unity Editor exactly while your game is paused and even more to close Unity Editor immediately after, then next time you'll open Unity Editor you'll have that value to 0 in project settings without even noticing.