I'm no expert on NCX files. Your conversion log states where Calibre sees the problem though:
Code:
Indexing navPoints ...
*** TOC discontinuity: nodes are not sequential ***
node 000: 'Cover' offset: 0x170D92 length: 0x9A
node 001: 'Title Page' offset: 0x64 != 0x170E2C
...
child 000: TOC: Cover --> OEBPS/xhtml/cover.xml
child 001: TOC: Title Page --> OEBPS/xhtml/title.html
child 002: TOC: Epigraph --> OEBPS/xhtml/epigraph.html
child 003: TOC: Contents --> OEBPS/xhtml/contents.html
child 004: TOC: PROLOGUE: SEPTEMBER 20, 1918 --> OEBPS/xhtml/prologue.html
child 005: TOC: 1. A LIVING CHRIST --> OEBPS/xhtml/chapter1.html
child 006: TOC: 2. NEUROSIS AND BEATITUDE --> OEBPS/xhtml/chapter2.html
...
_generate_indexed_navpoints: Failed to generate index
I don't know if the cause of this error is a bug or a problem with your NCX.
As a comparative example I do see minor differences vis-a-vis the one I just converted which worked (nothing jumps out at me though):
Code:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ncx PUBLIC "-//NISO//DTD ncx 2005-1//EN" "http://www.daisy.org/z3986/2005/ncx-2005-1.dtd">
<ncx version="2005-1" xml:lang="en-US" xmlns="http://www.daisy.org/z3986/2005/ncx/">
<head>
<meta name="dtb:PrimaryID" content="978-0-440-33516-0"/>
<meta name="dtb:depth" content="2"/>
<meta name="dtb:totalPageCount" content="0"/>
<meta name="dtb:maxPageNumber" content="0"/>
</head>
<docTitle><text>Outlander</text></docTitle>
<docAuthor><text>Diana Gabaldon</text></docAuthor>
<navMap>
<navPoint id="cvi" playOrder="1">
<navLabel><text>COVER PAGE</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_cvi_r1.htm"/>
</navPoint>
<navPoint id="tp" playOrder="2">
<navLabel><text>TITLE PAGE</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_tp_r1.htm"/>
</navPoint>
<navPoint id="toc" playOrder="3">
<navLabel><text>CONTENTS</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_toc_r1.htm"/>
</navPoint>
<navPoint id="ded" playOrder="4">
<navLabel><text>DEDICATION</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_ded_r1.htm"/>
</navPoint>
<navPoint id="epi" playOrder="5">
<navLabel><text>EPIGRAPH</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_epi_r1.htm"/>
</navPoint>
<navPoint id="qts" playOrder="6">
<navLabel><text>PRAISE</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_qts_r1.htm"/>
</navPoint>
<navPoint id="ack" playOrder="7">
<navLabel><text>ACKNOWLEDGMENTS</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_ack_r1.htm"/>
</navPoint>
<navPoint id="p01" playOrder="8">
<navLabel><text>PART ONE</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_p01_r1.htm"/>
<navPoint id="c01" playOrder="9">
<navLabel><text>CHAPTER 1</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c01_r1.htm"/>
</navPoint>
<navPoint id="c02" playOrder="10">
<navLabel><text>CHAPTER 2</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c02_r1.htm"/>
</navPoint>
<navPoint id="c03" playOrder="11">
<navLabel><text>CHAPTER 3</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c03_r1.htm"/>
</navPoint>
<navPoint id="c04" playOrder="12">
<navLabel><text>CHAPTER 4</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c04_r1.htm"/>
</navPoint>
<navPoint id="c05" playOrder="13">
<navLabel><text>CHAPTER 5</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c05_r1.htm"/>
</navPoint>
</navPoint>
<navPoint id="p02" playOrder="14">
<navLabel><text>PART TWO</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_p02_r1.htm"/>
<navPoint id="c06" playOrder="15">
<navLabel><text>CHAPTER 6</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c06_r1.htm"/>
</navPoint>
<navPoint id="c07" playOrder="16">
<navLabel><text>CHAPTER 7</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c07_r1.htm"/>
</navPoint>
<navPoint id="c08" playOrder="17">
<navLabel><text>CHAPTER 8</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c08_r1.htm"/>
</navPoint>
<navPoint id="c09" playOrder="18">
<navLabel><text>CHAPTER 9</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c09_r1.htm"/>
</navPoint>
<navPoint id="c10" playOrder="19">
<navLabel><text>CHAPTER 10</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c10_r1.htm"/>
</navPoint>
</navPoint>
<navPoint id="p03" playOrder="20">
<navLabel><text>PART THREE</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_p03_r1.htm"/>
<navPoint id="c11" playOrder="21">
<navLabel><text>CHAPTER 11</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c11_r1.htm"/>
</navPoint>
<navPoint id="c12" playOrder="22">
<navLabel><text>CHAPTER 12</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c12_r1.htm"/>
</navPoint>
<navPoint id="c13" playOrder="23">
<navLabel><text>CHAPTER 13</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c13_r1.htm"/>
</navPoint>
<navPoint id="c14" playOrder="24">
<navLabel><text>CHAPTER 14</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c14_r1.htm"/>
</navPoint>
<navPoint id="c15" playOrder="25">
<navLabel><text>CHAPTER 15</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c15_r1.htm"/>
</navPoint>
<navPoint id="c16" playOrder="26">
<navLabel><text>CHAPTER 16</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c16_r1.htm"/>
</navPoint>
<navPoint id="c17" playOrder="27">
<navLabel><text>CHAPTER 17</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c17_r1.htm"/>
</navPoint>
<navPoint id="c18" playOrder="28">
<navLabel><text>CHAPTER 18</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c18_r1.htm"/>
</navPoint>
<navPoint id="c19" playOrder="29">
<navLabel><text>CHAPTER 19</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c19_r1.htm"/>
</navPoint>
<navPoint id="c20" playOrder="30">
<navLabel><text>CHAPTER 20</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c20_r1.htm"/>
</navPoint>
<navPoint id="c21" playOrder="31">
<navLabel><text>CHAPTER 21</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c21_r1.htm"/>
</navPoint>
<navPoint id="c22" playOrder="32">
<navLabel><text>CHAPTER 22</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c22_r1.htm"/>
</navPoint>
<navPoint id="c23" playOrder="33">
<navLabel><text>CHAPTER 23</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c23_r1.htm"/>
</navPoint>
</navPoint>
<navPoint id="p04" playOrder="34">
<navLabel><text>PART FOUR</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_p04_r1.htm"/>
<navPoint id="c24" playOrder="35">
<navLabel><text>CHAPTER 24</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c24_r1.htm"/>
</navPoint>
<navPoint id="c25" playOrder="36">
<navLabel><text>CHAPTER 25</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c25_r1.htm"/>
</navPoint>
</navPoint>
<navPoint id="p05" playOrder="37">
<navLabel><text>PART FIVE</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_p05_r1.htm"/>
<navPoint id="c26" playOrder="38">
<navLabel><text>CHAPTER 26</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c26_r1.htm"/>
</navPoint>
<navPoint id="c27" playOrder="39">
<navLabel><text>CHAPTER 27</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c27_r1.htm"/>
</navPoint>
<navPoint id="c28" playOrder="40">
<navLabel><text>CHAPTER 28</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c28_r1.htm"/>
</navPoint>
<navPoint id="c29" playOrder="41">
<navLabel><text>CHAPTER 29</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c29_r1.htm"/>
</navPoint>
<navPoint id="c30" playOrder="42">
<navLabel><text>CHAPTER 30</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c30_r1.htm"/>
</navPoint>
<navPoint id="c31" playOrder="43">
<navLabel><text>CHAPTER 31</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c31_r1.htm"/>
</navPoint>
<navPoint id="c32" playOrder="44">
<navLabel><text>CHAPTER 32</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c32_r1.htm"/>
</navPoint>
<navPoint id="c33" playOrder="45">
<navLabel><text>CHAPTER 33</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c33_r1.htm"/>
</navPoint>
</navPoint>
<navPoint id="p06" playOrder="46">
<navLabel><text>PART SIX</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_p06_r1.htm"/>
<navPoint id="c34" playOrder="47">
<navLabel><text>CHAPTER 34</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c34_r1.htm"/>
</navPoint>
</navPoint>
<navPoint id="p07" playOrder="48">
<navLabel><text>PART SEVEN</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_p07_r1.htm"/>
<navPoint id="c35" playOrder="49">
<navLabel><text>CHAPTER 35</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c35_r1.htm"/>
</navPoint>
<navPoint id="c36" playOrder="50">
<navLabel><text>CHAPTER 36</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c36_r1.htm"/>
</navPoint>
<navPoint id="c37" playOrder="51">
<navLabel><text>CHAPTER 37</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c37_r1.htm"/>
</navPoint>
<navPoint id="c38" playOrder="52">
<navLabel><text>CHAPTER 38</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c38_r1.htm"/>
</navPoint>
<navPoint id="c39" playOrder="53">
<navLabel><text>CHAPTER 39</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c39_r1.htm"/>
</navPoint>
<navPoint id="c40" playOrder="54">
<navLabel><text>CHAPTER 40</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c40_r1.htm"/>
</navPoint>
<navPoint id="c41" playOrder="55">
<navLabel><text>CHAPTER 41</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_c41_r1.htm"/>
</navPoint>
</navPoint>
<navPoint id="bm1" playOrder="56">
<navLabel><text>Excerpt from Dragonfly in Amber</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_bm1_r1.htm"/>
</navPoint>
<navPoint id="bm2" playOrder="57">
<navLabel><text>An Intervew with Diana Gabaldon</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_bm2_r1.htm"/>
</navPoint>
<navPoint id="bm3" playOrder="58">
<navLabel><text>Reader’s Guide</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_bm3_r1.htm"/>
</navPoint>
<navPoint id="cop" playOrder="59">
<navLabel><text>COPYRIGHT PAGE</text></navLabel>
<content src="OEBPS/Gaba_9780440335160_epub_cop_r1.htm"/>
</navPoint>
</navMap>
</ncx>