Site Visibility setting is hiding blogs within the network

I’ve created a WP multisite + BP network and I’m using the Multisite Privacy plugin. The problem isn’t with the plugin, it’s with the Site Visibility option – “Discourage search engines from indexing this site”.

When a user selects this option (thus unchecking the “Public” box in the network admin view), none of the logged in users can see the site listed in the member’s Site list or their activity, etc.