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My opinion has aways been that this is a duplicate content problem with the 500 results that you can't see. But, at the end of the result set is the "include omitted results" link, and when you do the search including the omitted results you still can only see about 510 pages. (it adds 10 pages). I would think if duplicate content was the problem that the remaining 500 duplicate pages would show up when omitted results were included.
Any other theories out there on what causes this difference?