I’ve been using this plugin with my multisite setup for a while, allowing individual users to track their sites with individual tracking codes. I found the immediate issue with getting the options page to appear was that it was looking for a capability that single installation WordPress admins have (edit_users) but that multisite WordPress admins do not. (Superadmins, however, do).
This is similar to an issue I’ve seen with themes, where it checked for the “edit_theme” capability, which single install administrators have, but again, which multisite administrators don’t. In that case, checking for the capability “edit_theme_options” did the trick, because that’s something that all multisite admins should have. I’m not sure what the equivalent would be for plugins.