This is a follow up post from my post yesterday about click-through data in Webmaster Tools. After comparing some analytic data and reading numerous tweets and blog posts about the matter, it is obvious that there are discrepancies in the click-through data that is being shown in the Webmaster Tools interface in comparison to Google Analytic data and website logs.
Tom Critchlow from Distilled wrote an excellent post about this yesterday that you can read here: New Google Webmaster Tools Keyphrase Data Is 70% Useless
My take on this subject is as follows: This is a brand new tool released by Google a few days ago. There is obviously a discrepancy when the data is compared, but Google is not one to just sit around and take criticism. If they want this to be a valuable resource for webmasters, they will improve the tool so that analytic data and Webmaster Tools data matches. SEOs, including myself would really like this tool to provide a valuable metric that we can measure over time and use for further website optimization.