When extending a simple object which contains a jQuery object, the copy maintains a reference to the original object (demo).

var obj = {
        test: $('#test1')
    },
    copy = $.extend(true, {}, obj);
// copy maintains reference to obj
copy.test.addClass('red');

To get around this issue, I had to specifically clone the jQuery object, instead of extending the object.

var obj = {
        test: $('#test2')
    },
    copy = {};
// reference is not maintained
copy.test = obj.test.clone().addClass('red');

I read through the documentation and found this note on object wrappers

On a deep extend, Object and Array are extended, but object wrappers on primitive types such as String, Boolean, and Number are not.

If this does apply to this case, and this need falls outside of the extend function's behavior, then I guess I am not understanding the wording of the above statement.

This issue occurs in all versions of jQuery, all the way back to v1.2.6.