I had a similar Issue, I had multiple tables on a page and each had multiple datepickers, also on click of button "AddLine" it added a table row with dynamic HTML and datepicker.
I realized after a lot of search that my input date fields had no "id" defined they looked like this
<input type="text" class="datepicker" name="mDate1" value="" size=8 >
jquery was pointing all the date fields values to the very first date field defined on page, the calendar would popup on all the date fields but the value of 1st date field would change, I made a change to the html like this
<input type="text" class="datepicker" id="Date1" name="mDate1" value="" size=8 >
by adding a "id" and it started working, for the dynamic date fields I change the Id like this
var allColumns = $("#"+$tableId+" tr:last td");
$(allColumns).each(function (i,val) {
if($(val).find(":input").hasClass("datepicker")){
$(val).find(":input").attr("id",newId+$(val).find(":input").attr("id"));
}
});