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my last big site i designed had 4000 pages which didnt get immediatley indexed. once i got a PR 4 it seemed that it indexed one level at a time and some of the pages that were a few levels down didnt get indexed until i hit PR 5. I'm not sure if this is always the case but google seems not to always index pages with a low PR. Once the PR of a page improves it seems to get indexed for me (although sometimes completley random pages get indexed and others dont).
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