For what its worth:
CBR are compressed with the RAR-method, while CBZ are compressed with a ZIP-method. Kobo is very picky about the fact that the used compression method is expressed by using the according file-extension, otherwise the file won't show.
I've seen RAR compressed files faulty using the CBZ extension and ZIP compressed files faulty using the CBR extension. That won't matter on Windows system as Windows don't really use the file extensions, but it does matter for *nix systems.
You can check this by opening the zipped files with for instance notepad++ and look at the very first characters of that file:
- RAR indicates a RAR-method compressed file, so must have extension CBR
- PK indicates a ZIP-method compressend file, so must have extension CBZ