Sorry, Kovid, it didn't work. I commented out all the guide section, put the new content.opf file (otherwise unchanged) into the ePub package, validated and tested the new ePub, and converted as before. If anything the hyperlinks are even more unstable.
I then changed the guide section to one suggested on the mobi forum, went through the process again, and converted with Kindlegen. The links work, and this time I can get the Menu>goto>table of contents to work.
I've removed the old files from my first post, and attached the new files to this post. The files should all be dated 16/02/2013
I've deleted the fi