Now that I can add menus and content, when I try to use a shortcode to display the menu it doesn’t show up. I have tested the plugin on a standard installation and it works fine, seems to just be a multisite issue. The site I want to use it on isn’t the ‘main’ site, it’s an additional one.
I have the plugin activated on a single site in a multi site environment without problems and it is working fine.
I tried to activate it network wide in another installation and there I get the same issue as you have. I noticed that in a multi site install, all the menus of all the different sites are shown on every site, as well as in the network admin section.
Seems to me that it doesn’t support a network wide install.
I would suggest looking into the single site activation once more and find another solution for the permission problem. As I said, in my multi site installation, single site activation worked fine.