Worked this one out
$("body").on("show", ".bootbox", function () {
/* Dont add header again if div has been added */
if (!$(".modal-header")[0]) {
$(".bootbox").prepend("<div class=\"modal-header\"><a href=\"javascript:;\" class=\"close\">×</a><h3>Confirm Delete</h3></div>");
}
});
Basically prepend is called as the bootbox is launched, so by the time the modal is visible the title has been added. Also had to add a check to make sure the title is only appended once