Eric Koleda from the Google AdWords API Team replied basically pointing fault at the tool.
I think the problem here lies in the Keyword Tool's web interface.
You'll notice that changing the match type drop down from Broad to Phrase or Exact does not change the estimated position or average CPC. It is unlikely that the match type has no effect on these parameters, and in the API changing the match type does change the returned position and CPC values. My guess is that the web tool is always using the Broad match type for getting estimates, and that the numbers returned by the API are accurate.
I validated that the Google keyword tool does not change the estimated position or average CPC when you change the match type from broad, exact, or phrase types. Logically, it would make sense that this means the keyword tool is off when reporting on those factors and narrowing the results by match type.
It seems if you want to get more accurate numbers for estimated position or average CPC you would have to use the AdWords API.
Forum discussion at Google AdWords API Help.