What is the cause of this scenario? Site:http://www.example.com/folder/ shows 1,000 total results (showing 1-100 of about 1,000 from example.com) But, when you view at 100 results at a time you can only browse through about 500 results before reaching the end.
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?
They always keep turning the dials, so it's entirely possible that they're simply not showing the entire results set at any particular time. Another thing is that if we can only see 500 or so, we can't examine the very end for pages that are 950+ can we?