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It seems like you did everything right on the CM side of things. Just to double-check, verify that you have a "collections.json" file in the "system" folder of the Kindle, and that it looks half-way correct (much of it is just seemingly garbage numbers (UUIDs, ASINS, and such, but you should at least find the collection names in there).
I can't really help you with the calibre side of things, but I remember that it needs a little bit of setup before you can use it properly. Maybe that is what you are missing. Please refer to the calibre plugin documentation... IIRC, the plugin can also show details about what it did (like number of imported collections etc.)
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