Well I was able to do a work around and it seems to be tracking it now.
I added the following code to my footer and it works well:
jQuery(document).ready(function () {
var hashtag = /#\S+/
jQuery('.menu li a').click(function(){
var match = jQuery(this).attr('href').match(hashtag);
ga('send', 'pageview', '/' + match[0]);
})
});
If anyone has any better suggestions, I'm still willing to try it out.