For those of you that are still having this problem, I found the naughty, duplicate <head> code in a separate file located outside of the rest of the PHP files: wp-blog-header.php in the root WP directory.
The problem occurred because I was using a favicon and didn’t put it where it should go: the header.php file.
I also ended up having to use feedburner to make it clickable for users as without it still brought an invalidated error even though w3 said it was valid.
I explain everything in detail on my blog here.
I hope this helps.
