Drupal 7 Omega - js file not working
You need to wrap your javascript in a Drupal Behaviors handler. You can read the Javascript Documentation for more information (scroll down and look for the heading "Behaviors"). 

Basically, your code will end up looking something like this:

    (function ($) {  

      Drupal.behaviors.exampleBehavior = {
        attach: function (context, settings) {            
         // All your code here
       }
     };

   })(jQuery);


If this does not solve your issue, you use check your site for any javascript error messages and update your original post to include them. The way I recommend to do this is to install the Web Developer plugin for Firefox and open up the Error Console (tools -> web developer -> error console) and look for messages highlighted in red.