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Have you checked the response code on the pages that are not indexed? You may want to try something like LiveHTTPHeaders, a Firefox plugin, that you can detect what the HTTP response code of the page is. If you are not getting a HTTP 200 Status OK, that could be why the page is not getting indexed.
This usually is a problem with a whole domain using a CMS and something isn't correct, but could happen on a particular page depending on your coding. If anything, you should always check your HTTP status response if you are having indexing problems. It could be as simple as a >, ", or < in the wrong place.
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