I've used this plugin before and it worked as expected, but I did just run into a similar issue using a different plugin (and theme), so this topic is fresh in my mind right now. Here are a couple of things that may help, since the dev has responded to you yet:
2. This page goes over various approaches to deciding which file to put the GA code in. http://www.wpbeginner.com/beginners-guide/how-to-install-google-analytics-in-wordpress/
3. If you run your site through a code validator (like this one: http://validator.w3.org/) you'll see why your GA ID is actually showing up on the site instead of being hidden. (There are about 20 errors, most of which deal with stray / improper tags in the header.)
4. Lastly, if you can't get the plugin to work, these two are good alternatives:
Hope that helps.