Confused about Internal Links in Google Webmaster Tools

1. Google has over 1400 pages indexed for one of my sites (based on a site: query).

2. In the "Links to your site" section in Webmaster Tools, it lists over 400 links from the that same domain.

3. Yet in the Internal Links section, it only shows 14 internal links.

Besides the fact that #2 seems to contradict #3, does anyone have any experience with a factor that would stop google from considering something as an "internal link", even though it counts it as a link from the domain to the same domain?

A further bit of info, that Internal Links section has changed a lick in months. While every other piece of info seems to change daily or weekly.

This has been discussed over half a dozen times, mostly in the past week or 2. Search the forums you'll find your answer. Also, good rule of thumb is to use the Yahoo! Site Explorer tool for a more accurate count.

I do use Yahoo site explorer for backlink checking.

The point is that Google crawled from the root page through to over a thousand internal pages, so it clearly knows that there are internal links involved because it itself has found them.

(I do take pride in searching before posting but I was unable to find anything that addresses this particular question. I apologize if I missed something.)