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James - if you're using bookmarks and anchors/links for the table of contents then what matters is what you name the bookmarks. So name your main Chapter One bookmark "chapterone" and the one in the sample "samplechapterone". Or something along those lines, I'm not 100% clear what each of the ereaders does automatically with bookmark names. I know that would work for mobi/kindle format. At this point, I wouldn't recommend doing a toc any other way (I can't remember if you mentioned how you're creating your toc).
It's definitely odd that the headers aren't any bigger - I seem to be doing the exact same thing and mine are. But I can tell you I would be at least as frustrated as you are if I had run into the same problems.
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