Bootstrap doesn't use "checked" attribute of checkbox

You could use prop. I faced the same issue. On checking a checkbox, the attribute checked came as undefined. When i changed it to prop, it gave true and false value based on the state of the check box.

$('#checkboxId').prop('checked');

If I am understanding your issue I think the answer to an older question should help.

$('#toggle-all').click(function() {
    $('.btn-group input[type="checkbox"]').prop('checked', true);
});

http://jsfiddle.net/mmfansler/g3mu8/

this work for uncheck

jQuery('span', $('#uniform-You_id_checkbox')).removeClass("checked");

$('#You_id_checkbox').removeAttr("checked");