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I've had these issues on the Glo and now with the Aura, except with firmware 2.5.1 or 2.5.2 (don't remember) when setting the margins to zero.
I'm copying my epubs directly onto the SD card (no directories) usually without connecting the reader to the computer.
Since buying the Aura, I've copied all my books directly to the Glo using Calibre into the main memory, and in a short test I couldn't reproduce the font change anymore. The page numbers in the margins don't show up either.
Is there a way to configure Calibre so that it doesn't copy the books into directories and subdirectories on the device or SD card?
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