Webmaster tools on Google are perhaps the best way of tracking your site's performance. Unfortunatley, like everything else, it sometimes goes wrong but unlike some reporting sites, Google issues heads up statements and come clean.
Quote: 'The search query data shown in Webmaster Tools for the month of June may not be complete for some sites at the moment. We are aware of this issue and are looking into it; you do not need to take any action. We hope to have the full data shown again in the near future. This will have no effect on your site's performance in search results. Thank you for your patience. Update: This issue is now resolved and all missing data has been restored' Read blog post (June 10th 2010 and resolved June 24th 2010)