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I've found that some books that I've built and cause this problem cause less problems if I strip out javascript and other unnecessary stuff -- which contributes to the code complexity and size theory I think. Books (i.e., downloaded web pages) with lots of javascript cause more problems even if they are small.
If it is stuffing info in the database, is there any chance the calibre kobo driver could precalculate this stuff and put it in the database instead? Maybe on a single shot basis when a book is causing issues...
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