Yes, I understand completely. So, I reinstalled it and used the work-around to just switch templates, create pages with the Nav Menu Roles settings, then go back to my initial template. It works really well.
Again, I have to say that the development of this plugin was top-notch! Good job!
It conflicted with Shape5 Vertex theme, not WordPress. I am using 4.3.1 and if I disable the template (as the work around in the FAQ stated) then re-enable the template, it works just fine.
