Change this:
$(".boxtwo").draggable({ containment: "#containment-wrapper", scroll: false });
$(".boxthree").draggable({ containment: "#containment-wrapper", scroll: false});
to this:
$(".boxtwo").draggable({ containment: "#containment-wrapper", scroll: false });
$(".boxthree").draggable({ containment: "parent", scroll: false});