You need to attach your js using Drupal behaviors.

Drupal.behaviors.yourmodulename = {
  attach: function (context, settings) {
    // This code is run on page load and after every ajax request
    // attach colorbox functionality here
  }
};

I found this blog post on the subject really useful.

You need to attach your js using Drupal behaviors.

Drupal.behaviors.yourmodulename = {
  attach: function (context, settings) {
    // This code is run on page load and after every ajax request
    // attach colorbox functionality here... 
    // the following line should do the job but I've not tested it
    // we are using context so it only applies to the newly added objects
    $('.colorbox', context).colorbox();
  }
};

I found this blog post on the subject really useful.