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It seems to happen randomly for me, which is why I am having so much trouble tracking it down. The last time it happened (when I posted to ask about it), I reimported the original epub and ran it through Modify ePub, ticking just one box each time, and had no problems. It's not a big deal for me to check the order of files against the original, since it happens so rarely, but it would be nice to figure it out.
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