Last week Google announced a change to the way they classify internal and external links in Webmaster Tools. The update shouldn’t change the number of links, but should report your links in a more accurate way in regards to where they are coming from.In the past, links from subdomains (ie: example.seo.com) were classified as external links. Even a link from the non www version of your site was classified as external. With the changes, links from these types of domains will now be considered internal links, as long as you also own the root domain.
With this change you may notice your total number of external links go down, but this is only because some of your links that were previously classified as external are now being classified as internal. Your total number of links should remain the same.