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What model Kindle? If I assume a Kindle 3 from your profile... what setting is your Kindle set to when you look at those books? Is it set to sort by Most Recent, Title or Author?
If you set it to Most Recent, obviously that is a useless setting for Kindle owners to keep series order.
If you set it to Author, then the Kindle will sort by Published date reversed. So whether books appear in correct order is down to the metadata you have in calibre.
if you set it by Title, then the Kindle will sort alphabetically. I've never had an issue with this. Are you using a metadata plugboard to set your book titles to include the series information (the recommended approach)?
As for your second question about books missing, the general theory is to try restarting your device, and if that doesn't work delete the book and send it again.
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