From Webmaster Tools FAQ:
Q: The Search Queries feature says that my site ranks #5 for [cookies], but when I search for [cookies] I see it ranking #8 (or I don't see it at all). What gives?
A: Several things:
Different searchers can see different results, based on things like
where they're searching from (geographic differences), personalized
search factors, momentary fluctuations, etc. The Search Queries data
is an average of these searches, so you may not see the same ranking
when searching for that keyword right now.
You may be looking at
searches done on multiple Google properties (Web Search, Image Search,
Mobile Search, etc.) and from many countries (google.com,
google.co.uk, google.fr, etc.). Your site may rank highly in Image
Search but not in Web Search, or may rank highly in Argentina but not
in the US. All of this gets averaged together on the main Search
Queries page. You can filter the data shown using the drop-down menus.