How to clone a jQuery Chosen select box with dynamically populated options?-Collection of common programming errors

It seems that the problem is that the clone is still sharing some data with the original object. From the Jquery docs http://api.jquery.com/clone/

Normally, any event handlers bound to the original element are not copied to the clone. The optional withDataAndEvents parameter allows us to change this behavior, and to instead make copies of all of the event handlers as well, bound to the new copy of the element. As of jQuery 1.4, all element data (attached by the .data() method) is also copied to the new copy.

However, objects and arrays within element data are not copied and will continue to be shared between the cloned element and the original element. To deep copy all data, copy each one manually:

var $elem = $('#elem').data( "arr": [ 1 ] ), // Original element with attached data
$clone = $elem.clone( true )
.data( "arr", $.extend( [], $elem.data("arr") ) ); // Deep copy to prevent data sharing

Hope this helps