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followgreg - 2:16 am on Oct 19, 2007 (gmt 0)
Ever since we had a proxy hijack many pages never reapeared in GWT. And the latest Google.com site: query shows that many pages are totally gone awol again. You may be in the same situation. I too went through the process of checking our servers, hired security experts and everything, found nothing.
Did you take a look at your GWT internal links?
It's like we are penalized now for what others did to us long time ago.