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I have seen these type of results before if the depth and number of links has not been set before you index a web site, perhaps you should check the settings in the admin panel for what depth and number of links to be indexed.
One other thing to try is to use the update site feature which sometimes re indexes better the second time around, it will just mark a red cross by the page if it has already been indexed.
When I fisrt index a web site I go in quite shallow and follow it up a while later with amuch deper index.
Give it another try it should be okay
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