Ok now i'm seeing something that makes sense.
Google webmaster tools, now shows your keywords, number of searches, your search position etc.
In the one website I checked where i'm on page one for a number of particular search terms, the number of searches corresponds with the number of exacts on the GKT.
So maybe the GKT is accurate, presumably they're using the same stats for the GKT as for Webmaster tools. The one thing they say is that they now only include direct Google searches in GKT not Google search partners like they did before