Per-site options problem

There are a couple of ways you could do that.

a) Activate the plugin on all sites except the main site. Right now you probably have it network activated. You could deactivate it and then activate it on each sub-site, one by one. Remember to change the “Multisite settings” option to “Global”.

b) Instead of completely hiding a menu item with the “Show/Hide” button, change the required capability to “super_admin”. This way you will still be able to see it (on any site), but normal administrators will not.

c) Use the Pro version to do the same thing as b). It’s easier in the Pro version because you can just click a bunch of checkboxes instead of manually changing the capability for each menu item.