Originally Posted by nickredding
I have abandoned this now ...
Like a bug attracted to the light I went back to this yet again and I have found a solution. I had already discovered that Amazon uses two slightly different formats--one generated by Kindlegen and one generated by the Amazon periodical platform that is used for subscriptions. They are different (but they both work properly on the K3 Sections and Articles view). I have found the key aspects of the Kindlegen format and I can reproduce it using the Calibre MOBI output code. It turns out that (for Kindlegen-generated documents) the Kindle expects some TOC markup within the HTML as well as the binary table of contents information in the header. I'm going to have to look at Kovid's new MOBI writer code to see how the Kindle requirements can be accomodated without breaking any other MOBI readers.