What happens if you remove 'Response.ContentType = "application/pdf"' but keep 'Response.ContentType = "text/html"'?
Or try something like this:
protected override void Render(HtmlTextWriter writer)
{
var strWr = new StringWriter();
var htmlWr = new HtmlTextWriter(strWr);
base.Render(htmlWr);
htmlWr.Flush();
var htmlToPdf = new HtmlToPdfConverter();
htmlToPdf.GeneratePdf(strWr.ToString(), null, @"c:\AlertAttachments\example2.pdf");
base.Render(writer);
Response.ContentType = "text/html";
}