Not sure about the real situation, because the js files are packed in the website and it's hard for me to tell from the source code. However, there is some clue you may find useful.
I assume you want to run the js script after the template is rendered. In this case, you need to write like this.
Template.nav.rendered = function() {
// Run the js to render the dropdown or whatever.
}
This is the Meteor programming paradigm. If you simply run the js files directly, the template may not be ready when you run that part of the code. The "rendered" callback is the place you need to place some actions after this template is ready.
In addition, you can refer the official document here http://docs.meteor.com/#template_rendered