Thanks for the reply. I am following the Kindlegen instructions. and selecting the html file. All of the bits listed are in the correct bits with the html file in same folder that I navigate down to and then generate the mobi file. It must know the opf file is there because I had some errors which I corrected in the opf file and when I generated the mobi file again it just came down to the cover and it not finding the ncx file.
I have generated this file with mobipocket creator and it passed with no problems so I know the TOC NCX file is Ok. (This book has some extra features like embedded fonts that I would like to take advantage of that is why I am generating a file using Kindlegen so that the fonts etc can be seen on the Kindle fire etc)
I have taken a screenshot of the folder everything is in and attached it just to see if anybody can see if I have that wrong.