You already have some of the answers, but...
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Originally Posted by AlexBell
I have in front of me Can You forgive Her? by Anthony Trollope which I put on the MR Library recently, both opened at Chapter 1 on my Sony PRS T1 and the Kobo Touch.
On the Sony the text appears as expected - the chapter title, a horizontal rule, and the text starting immediately below.
On the Kobo touch I see the chapter title and the horizontal rule, but the rest of the screen is blank - the text doesn't start until the next page.
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This is a known bug in the Kobo firmware and long paragraphs. If a paragraph exceeds a screen by a few lines, it will be pushed to start on the next screen. When I first went to chapter 1, the formatting was correct. When I increased the font size a couple of steps, the first paragraph was pushed to the next screen.
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Also, text which I have italicised shows in italics on the Sony, but shows in block (emphasised but in normal font style) on the Kobo Touch.
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As you have discovered, it is dependent on the font A couple of the built-in fonts are missing the italics. "Avenir" is one of them. "Georgia" works fine.
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The links seem to work without problem on the Kobo Touch in this and other ebooks of mine, though footnotes take some time to work.
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The links work for me as well. The only problems I had is with font and finger size for the footnote link. I use a smallish font and have big fingers. Pressing the footnote link isn't reliable for me. But when I increased the font size, it worked with no problems.
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I think I'll take a Kobo ebook apart and see if I can find clues as to the way Kobo does things.
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From what I can see, there aren't any real problems with your formatting. You have just managed to hit two well known bugs in the firmware.