The firmware and function on the two devices is identical, so the differences are elsewhere.
As books are going to the Aura as kepubs, that means you are probably using the KoboTouchExtended driver to send the books. Have you installed this recently? And if you have, the "Set Series information" option is probably not set. If this is set, you need to connect the device again as the series information is only set for books already in the library on the device.
If you want to read epubs, remove or disable the extended driver. And then check the settings of the KoboTouch driver to make sure they are what you want.
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