Calibre conversion does not take into account (apparently) the .opf options to correctly set Panel View: the ebook structure is standard, indeed, and Panel View is only activated upon setting a bunch of <meta> tags when defining .opf, the most important being
Code:
<meta name="book-type" content="comic"/>
So, if you are a little pratical you can do it by yourself, or use some tools like my
Kindle Comic Converter to perform conversion on your CBx files.