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I did a bit more investigating, and it turns out that all the books are being transferred; but the ePubs aren't showing up in the eReader list (even though they are there in the internal memory).
So sorry, it's got nothing to do with Calibre (I tried to delete the thread, but couldn't find a "delete" option - mods, please feel free to remove this thread!). I guess my eReader didn't come with the firmware upgrade that enabled to read ePubs; I'll have to go and install it.
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