A Drupal site that works fine for regular users returns a 404 not found error when I try to use the W3C validator on it; it is also not being indexed by google at all (which is the main issue but I suspect there is a connection). It is a https:// site with .htaccess rule to redirect any http:// request to the https://.

I had had it running in google webmaster tools and thought it was fine, but it turns out I had not added the https domain. After adding the https domain it's also returning the header as

HTTP/1.1 404 Not Found
Date: Mon, 15 Oct 2012 19:37:43 GMT
Server: Apache
Expires: Sun, 19 Nov 1978 05:00:00 GMT
Cache-Control: no-cache, must-revalidate, post-check=0, pre-check=0

Robots.txt just has

User-agent: *
Crawl-delay: 10
# Files
Disallow: /cron.php

How can I check what the issue is here?