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It's best practice to only have one home page variation. Google won't be able to tell which is your main page and you will also get duplicate content issues etc. If you haven't already I would redirect the /default.asp pages to the root domain. As for your original question it does seem a bit odd that they are different scores but I would imagine it's because your main root domain would have more backlinks to it compared to your /default.asp pages.

On a given website, it is better to get links from the higher PA pages (all of the pages will have the same DA). So a homepage link for example (which will usually have a higher PA than other pages on the site) will be better than a link from a deep, newly created page (which is likely have a low PA).

There are a number of tools that will help you with identifying the problematic backlinks. Kerboo (formerly Link Risk) is very good and one of my personal favourites to simplify the process. Alternatively, use URL Profiler. This (I find) more complete and allows me a little more control in how I audit the links, but it depends what you want to do. In my opinion, both are about the best in their class and well worth a look. -Andy

Hi gardenbeet.com had the same problem about 4 years ago - do not be alarmed. It just means that the internal page has (probably) higher value links than the home page . At the time I was advised to look at my site architecture to ensure the link juice gets distributed around the website (at least as evenly as the home page would redirect the juice)  (not sure if that point is still relevant).

Agreed with Chris that some context would help. This is a big, complex decision, and it's tough to judge link quality without seeing the links. My gut feeling is that a bunch of foreign Blogspot dofollow links probably are spammy, but there's a big difference between fixing a link-based penalty, preventing one, and just taking a hatchet to your links.

No I do not need to type in /default.asp on the end to bring up the homepage.  So having this setting enabled would cause SEO problems correct? Right now we have versions of our hompage as follows: www.domain.com http://www.domain.com resoves to www.domain.com http://domain.com resolves to http://www.domain.com/Default.asp If you click on the home button on our site you get www.domain.com/default.asp