app.js

//in your application, rather than using window.location to get the current url
App.getLocation = function(){
    return window.location.protocol + '//' + window.location.host 
              + '/' + Backbone.history.options.root + Backbone.history.getFragment()
}

bootstrap.js

//when your application starts up
Backbone.history.start({ pushState: Modernizr.history, silent: true });
if(!Modernizr.history) {
    var rootLength = Backbone.history.options.root.length;
    var fragment = window.location.pathname.substr(rootLength);
    Backbone.history.navigate(fragment, { trigger: true });
} else {
    Backbone.history.loadUrl(Backbone.history.getFragment())
}

Fixed the IE problem