Calibre not sending correctly converted book to device

I am trying to add a book to my Kindle. I am accustomed to using Calibre and have had no problems in the past converting books.

The document is on notebook format and I have been using / to bracket words to be shown in italics and -- as an emdash. This has worked in the past.

I am currently working on Magic Inc. by Robert Heinlein. When I open the book on Calibre and check it everything appears to be fine - the italics & dashes are there, the lines between paragraphs have been deleted etc. and the book appears in the correct place in my Calibre library

However the version that appears on my Kindle still has the line space between the paragraphs, words intended to be in italics are not (and the words themselves appear with the slashes visible e.g. /italic/), the dashes remain as two hyphens and the book itself does not appear in the correct location (alphabetically by author) but at the end after the dictionary etc.

I have recently upgraded my computer to Windows 10 and wonder if I should be using a different version of Calibre, I have two versions on my computer at the moment: Calibre 2.43 and Calibre 64 bit 2.44.1, neither delivers the book to the device correctly.

I shall have another go now and see what happens!