No need, I started working on MOBI indexing a few days ago. Hopefully I will be able to figure out the problem. I've written code that decompiles the MOBI, including all indexing information which should allow me to see what the differences between kindlegen generated periodicals and calibre ones are. You can run it with
calibre-debug --inspect-mobi filename.mobi
You will need to be running from latest calibre source for this to work.
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