[DNSB]

You will need to either split the files at the sections or use IDs to locate the section headers. All your current links are pointing to the same file which suggests that your sections are in the same file as the chapter header with no way to differentiate them.

  <h1>Chapter 1</h1>

  <h2 id="section0001">Section 1</h2>

  <h2 id="section0002">Section 2</h2>

  <h2 id="section0003">Section 3</h2>

  <h2 id="section0004">Section 4</h2>

  <h2 id="section0005">Section 5</h2>

  <h2 id="section0006">Section 6</h2>

<navMap>
  <navPoint id="navPoint1">
    <navLabel>
      <text>Chapter 1</text>
    </navLabel>
    <content src="Text/Section0001.xhtml" />
    <navPoint id="navPoint2">
      <navLabel>
        <text>Section 1</text>
      </navLabel>
      <content src="Text/Section0001.xhtml#section0001" />
    </navPoint>
    <navPoint id="navPoint3">
      <navLabel>
        <text>Section 2</text>
      </navLabel>
      <content src="Text/Section0001.xhtml#section0002" />
    </navPoint>
    <navPoint id="navPoint4">
      <navLabel>
        <text>Section 3</text>
      </navLabel>
      <content src="Text/Section0001.xhtml#section0003" />
    </navPoint>
    <navPoint id="navPoint5">
      <navLabel>
        <text>Section 4</text>
      </navLabel>
      <content src="Text/Section0001.xhtml#section0004" />
    </navPoint>
    <navPoint id="navPoint6">
      <navLabel>
        <text>Section 5</text>
      </navLabel>
      <content src="Text/Section0001.xhtml#section0005" />
    </navPoint>
    <navPoint id="navPoint7">
      <navLabel>
        <text>Section 6</text>
      </navLabel>
      <content src="Text/Section0001.xhtml#section0006" />
    </navPoint>
  </navPoint>
</navMap>