Al,
The Autotune functionality uses the website address that you're currently accessing the administrator area of your site from to recommend the Site, Domain, and other settings for your Facebook Application.
So, if your site is
www.blah.com, but you're accessing the administrator area directly from the IP address of
123.123.123.123/administrator, then the recommendations will all use 123.123.123.123 as the site's address. Generally, that won't work for Facebook Applications because they want a real domain name. If you for some reason can't access the admin area of your site using the domain name (I can't imagine why), you'll need to manually configure the app settings. In that case, simply replace our recommended settings of the IP addresses with the actual domain name of your site.
Hope that helps. If you're not accessing your site using an IP address, but still getting recommendations with IPs, that's definitely strange... let us know, and we'll help with that too!
Thanks,
Alex