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I'm dredging from deep memory - but I think a similar issue was brought up on a Battery Life Issue thread - indexing running down a battery. Anyways - someone mentioned the format of a book (and also the size) affecting the indexing. Are the non-indexed books Kindle books or from a PD site? If non-Kindle, you may want to find the older thread for clues as to indexing being affected by book format.
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