I don't read comics, but, I've tested them enough to know that both CBR and CBZ work. And, I've never had a problem adding them to the device.
The only thing I can immediately think of is the file names involved. If you are sending form calibre, it should be making sure the file name of the book is correct. But, it might be the file name of the images inside the book. I would probably need to see one of the files to work it out.
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