Messing around with the plugin and I first installed WP at subdomains and when I created new networks I was able to visit that new networks "network" settings page.
Example subdomain install:
network.example.com (can view at network.example.com/wp-admin/network/)
Example (issue) subfolders:
network.example.com (redirects to example.com/wp-admin/network)
Trying to access any of the new sites at network/site-info.php?id=1 and changing the ID just states no user privilege.
I did not have this issue when MS was a subdomain install. I need the network to be subfolders so each new network can be a subdomain and all sites in that network be subfolders.