First your code is few issues, Any way try this,
JsFiddle Example
$(function() {
var counter =2;
$("#addButton2").click(function () {
var newTextBoxDiv2 = $(document.createElement('div')).attr("id", 'TextBoxDiv2' + counter);
newTextBoxDiv2.after().html("<table width='1200' border='0' cellspacing='0' cellpadding='0'><tr><td>Date</td><td><li class='demo'><div class='box'><input class='multi' type='text' id='from-input_"+counter+"' maxlength='10'></div><div class='code-box' style='display:none;'>$('#from-input').multiDatesPicker();<pre class='code prettyprint'></pre></div></li></td></tr></table>");
newTextBoxDiv2.appendTo("#TextBoxesGroup2");
$("#from-input_"+counter).multiDatesPicker();
counter++;
});
});