You probably are using the jQuery(element).load(url) method.
jQuery uses the browser's .innerHTML property to parse the retrieved document and insert it into the current document. During this process, browsers often filter elements from the document such as , , or elements. As a result, the elements retrieved by .load() may not be exactly the same as if the document were retrieved directly by the browser.
Try to scope the content that you are receiving from the server, for example:
// will load only the content inside the element with id="container"
jQuery(element).load("yoururl #container");
You probably should try to execute the JS code from the script, using the complete callback, for example:
jQuery(element).load("yoururl #container", function(response, status, xhr) {
do_stuff_after_load();
}