lucy24 - 9:51 pm on May 6, 2013 (gmt 0)
Same as the difference between http and https on google, isn't it? Except that GA recognizes its own name so it knows the difference between a search and a direct referral. I get the same thing on piwik: google dot com shows up as a "referring site", completely separate from "searches". And it sure as ### isn't because Matt Cutts has been talking about me in a blog ;)
Unless I have completely misunderstood the question.