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Are the pages in the subdirectories linking to your site? Remember , PhpDig only follow's links , it cannot manually find all the pages from your site, if the linking doesn't work, create a new MySQL database and then try, I had a problem where PhpDig wouldn't index a site when it was already re-indexed 5 times in the history, I re-installed in on a new database, it worked, Check and see.
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