That's a known bug in the mobi format. Move the anchor-point which the href in the toc.ncx entry points to before (and outside of) the block element you're linking to.
If the href in the ncx is "Text/your_html_file.xhtml#chap1"... then the code at that point in the html should be something like:
Code:
<a id="chap1"></a><h1>Chapter 1</h1>
as opposed to:
Code:
<h1 id="chap1">Chapter 1</h1>
Also, this bug won't rear it's ugly head if your chapters are all separate html files. In other words, if the links in the ncx file all just point to a unique html file (with no fragment identifier in the url), this won't happen.
NOTE: I didn't get a chance to view the source to see if this is the exact problem. It just sounds very similar and the bug bites quite few people.
Quote:
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Originally Posted by Doitsu
Your source file contains Mobipocket tags that are no longer supported by Kindlegen
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Out of curiosity, what tags are being used that kindlegen no longer supports. Most of the old mobipocket tags are still perfectly functional/valid with kindlegen, to my knowledge.