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See also: Navigation goes to the wrong section on Kindle
Clicking on a link in a Kindle book (for example, from a footnote back to the original reference) sometimes seems to go to the wrong location, especially within long paragraphs.
For Kindle books, Jutoh moves bookmarks within a paragraph to the start of the paragraph, so if you have a long paragraph, the viewing position will be some way from the actual bookmark position. This is to work around bugs in Kindle that cause formatting glitches if you navigate to a bookmark that's actually within the paragraph, and even the Amazon guidelines recommends putting bookmarks at the start of the paragraph:
kindlegen.s3.amazonaws.com/AmazonKindlePublishingGuidelines.pdf
(3.9.2 HTML Guideline #2: Anchors Must Be Added Before Formatting Tags).
If you switch to Epub compilation, Compile, then open the Epub in Kindle Previewer, you'll get a mobi without the Kindle optimizations, and the links appear to work better. However, this goes against Amazon recommendations and may cause formatting glitches after navigation.
Contents | Start | End | Previous: KB0090: I split a document and now there are unresolved bookmarks | Next: KB0092: Executing custom commands before and after compilation