Google announced, via its Webmaster Central Blog, that it was making an update to the “Top Search Queries” data. Beginning today, Google Webmaster Tools Top Search Query report will take the average of a site’s top URL rankings for a query versus an average of all results for a site’s URLs on a given query. For example, if your website about gadgets showed up today as the 3rd, 7th, and 11th results on a Google search for “cool gadgets,” Webmaster Tools would take the average of 3, 7 and 11 and the report would show an average position of 7. Starting today, Webmaster Tools will show an average position of 3 for the same query.
Of course, it will also take this average over multiple queries within a given time period but your average positions should start improving, going forward. Your historical data will not change, according to Google.