luuna31 - 3:39 pm on Aug 20, 2012 (gmt 0)
The SEO queries report and the Organic keywords report are different because they are not reporting the same data.
Traffic Sources>Search>Organic shows you the keywords which drove traffic to your website and how that traffic interacted with your website (bounce rate, pages/visit, etc.) whereas Traffic Sources>Search Engine Optimization>Queries shows the number of times your website appeared in a search engine result list for any given keyword, including the number of click-throughs to your site and the average position of your website within that result list.
Hope this makes sense.