It seems a bug in the IIS SEO Toolkit, it doesn't seem to be able to handle the html 5 doctype.
With this doctype it stops crawling after just the home page and reports violations that do not exist.
When I change the doctype to xhtml it crawls the site as it should and reports true violations only and no false violations.
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" >
doctype is controlled at the skin level in the layout.master file.
I will report this issue to Microsoft.