I've been using Google webmaster tools and have a site added and verified. Its been in there a while but I noticed that it reads there are no links either external or internal. This can't possibly be correct because it ranks really high for competitive terms in Google and other link checking tools read many thousands of links.
Google love new content. Google rank new sites and new pages high in search results, but only for few days, after some time, new sites just vanish from search results. The internal and external links update after some time. You need to wait for some time, to see links in webmaster tools.
The site is more than a year old and if it had lost all its links it wouldn't be ranking high anymore! I guess if you're having the same problem Nestrer then there must be a problem with Webmaster Tools.
I've been using Google Webmaster Tools for over 2 years and internal/external links has always worked for all my sites, so I don't think that it's broken. The only time it hasn't worked is when a site isn't verified correctly.