Your code has multiple doctypes, multiple <body> sections, </html> in the middle of the document.... all stuff that isn't allowed. Here's the validator report, which will show you the various errors.
Thanks for the reply. I have looked at the index.php for the errors listed but cannot seem to find them; does the validator page validate the whole site or just the index.php?
The validator will validate one page at a time; the link I gave was just for your home page. It doesn't matter whether it's generated from php versus a native html file. Not sure why you can't see it, but how about doing a "view source" in your browser?