If I understand correctly it seems like IIS SEO is not able to crawl anything from your site, right?
When you are in the report and you use the menu "Report->New Query" and Press Execute, do you only get two URLs? Could you add the Column "Is External" and see if they are treated as External?
It could be that the Start URL you are entering is not matching the criteria for "external pages" used in the "New Analysis" advanced settings. If that is the case then when you start a new analysis could you make sure that you expand the Advanced Settings and make sure that the "Consider as internal link..." matches the criteria that would crawl your site.
Also, could you see if in the Violations->Summary there is something about using Noindex/nofollow?
Could you also see what is the content in the URLs that were crawled and see if we found links on them? (Double click and see "Content tab" and "Links Tab"), Is the Content Type set correctly to HTML.
I am not familiar with Sitefinity, but if you send me an email at microsoft . com (same user as in this reply) and you can send me either the content of the HTML of the start url or a link to your site I can try to look at the problem.