I might be off but...
On sites hit by penguin, is anyone noticing that the site:domain.com query returns only 492 results when you reach to page 50? On page 1 and first set of pages, it looks like the full index is there.
I see it happening with one site of mine, hit in the May update. I also went through a couple of sites from google support forums and found two that also have only 492 results when you reach page 50. And another that had 491.
On the 50th page, you get the "In order to show you the most relevant results, we have omitted some entries...". Clicking on the link to view the omitted results shows a few more pages, but not the vast majority of pages that should be there. These four sites all have much more than 492 indexed pages. One of them, has 66,000 pages of content (not thin or user profiles or anything like that)