Ajax on Add another item of field collection
Sounds like you need to use Drupal.behaviors and not just document.ready for your javascript.


  Drupal uses a "behaviors" system to provide a single mechanism for
  attaching JavaScript functionality to elements on a page. The benefit
  of having a single place for the behaviors is that they can be applied
  consistently when the page is first loaded and then when new content
  is added during AHAH/AJAX requests.


More info on Drupal.behaviors here