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Is there in the CSS perhaps a specific setting for justification of the p, html or body class? It could be, that iBooks does not do the inheritance quite well. If for example the p class is in the CSS setting the justification on, it should be overruled. However, it might be ignored for paragraphs.
I also seem to vaguely remember that you can do a setting to justify everything by default on the iBooks, in fact it is the default. Have you turned that off?
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