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This could also be due to intent based on what you're searches were; however, Google has given Google properties preferential treatment in the past as well. See: http://moz.com/google-algorithm-change "Dewey — April 2008 A large-scale shuffle seemed to occur at the end of March and into early April, but the specifics were unclear. Some suspected Google was pushing its own internal properties, including Google Books, but the evidence of that was limited."  Cheers!

Hi Thomas, I was wondering how you got on with this issue? Since it has been 5 months have you started to rank higher? Also, what were the types of links to your site (e.g. www.domain.com/?id=123456)? Thanks, Jason