If you create layers within layers, scene manager takes control over them even if you have not added them to the layer list:
So, if you create Sub layers the optimal solution would be if they stay visible or hidden as how you have set them to, the same way any object behaves. But if you switch between tasks in scene manager it unhides the Sub Layers within the task selected every time. So if you have a complex setup with a lot of layers you want to stay hidden they are suddenly visible again. The only way scene manager should treat these layers as “on” or “off” is if you explicitly add them to the layer list and switch them on/off there, if not the should stay as you have set them to in 3ds Max.
I hope you agree, and keep up the good work!