I was struggling with the Table of Contents feature and it was hard to find any help, even with the whole interweb in front of me.
Anyway, just by clutching at straws I discovered the Bookmarks window that I found contained bookmarks I'd never knowingly added. Clearing all the extraneous bookmarks might have done the job - just waiting on the export of a PDF...
Yay! That worked! /me dances!
In other news, the other thing that bugged the shit out of me in InDesign was the fact that my books constantly have warning triangles saying "you edited this document (a chapter of the book) outside the book!" It is *never* true but that doesn't seem to matter to InDesign. Anyway, the solution is as dumb as you might expect: If you have the Book window open while you edit, save and close your chapter, all will be fine.
Next problem, Updating the ToC is broken. Instead of going away to trawl the documents and then building the complete ToC, iD now does the trawl, but only builds the first page. Every time I have to manually add a new page and reflow text onto it, whereupon it builds the remaining pages (of which there are about 30 now). This one I haven't resolved and can get no help on aside from exporting to IDML and re-importing, which didn't work.
Problem 3. Do not make cross-references until the very end of your editing of your document. If you do it earlier you will find that typing slows down to one character per second appearing on-screen.
