I have noticed something pretty similar, although my screen is split into two sections, one is pages that your site has shown up for, and the other is actual clicks (which may be new - I don't remember seeing it before). When I click the link for the table of queries that my site ranks for, I usually do not see my site in the first three pages of results.
I probably should mention that I have not done any
SEO on the site, and in preperation for hiring an
SEO firm I wrote a script that logs every visitor to the site and records what search engine they came from as well as the search terms they used. I am still trying to reconcile that data with what is shown in webmaster tools, but at first look it does seem somewhat skewed.