Yes there will be conflicts with your current code when you include the master page
Now the current page html code surrounded with the ContentPlaceHolder1.
You need to change the javascript function for checkallBoxes to suit with this changes.
function should include like this
var RowCount=document.getElementById('ctl00_ContentPlaceHolder1_gvPresent').rows.length;
if the page use master page's ContentPlaceHolderID.
<asp:Content ID="content1" ContentPlaceHolderID="ContentPlaceHolder1"
runat="Server">