Crossed posts with Kovid and Itimpi - the Calibre viewer is not the best way to see if a Mobi file converted perfectly - in order to display it Calibre converts from mobi back to an internal format that's similar to epub.
Use the Kindle Previewer to see a book exactly as it will display on a Kindle with Navpoints, etc:
http://www.amazon.com/gp/feature.htm...cId=1000234621