I have just revisited three full size books and have followed the process of fixing them, both the font problem and the start issue. I am happy to report that all now work perfectly in the Previewer and on the Kindle 3 running v3.4.
So, for now, the issue is dealt with. I've kept the files created at each stage so it will be easy for me to test future Kindlegen and firmware versions.
Thanks to you all for the help.