Edit
To select an option in selectmenu, use the below.
$('#selectmenu_id option:eq(N)').prop('selected',true);
$('#selectmenu_id') .selectmenu('refresh');
Where N is the index number of the option.
You need to use .prop()
and then refresh each checkbox.
This will uncheck all checkboxes at once.
$('[type=checkbox]').prop('checked', false).checkboxradio('refresh');
This will go though each checkbox, in case you want to check/uncheck specific ones.
var checkboxes = $.mobile.activePage.find('[type=checkbox]');
$.each(checkboxes, function () {
$(this).prop('checked', false).checkboxradio('refresh');
});