About the Bug: I had the same bug with a full screen post process when I start my game in windowed in Unity.
The dirty fix I've got is in a monobehaviour :
void Start ()
{
if ( !Screen.fullScreen )
{
Screen.SetResolution(Screen.width, Screen.height, Screen.fullScreen);
}
}
I don't know if this is the same bug, but in case it is.
It's probably a texture or something like that, which isn't init properly. I don't think there is a proper fix without asking Unity guys to look into it.
PS: I'm reading your Game Design book, and there is very good ideas.
I will try your game soon !!