Created attachment 206137 [details]
XML file, FO output, and PDF

<?xml version="1.0" encoding="US-ASCII"?>
<!DOCTYPE book PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
"http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd">
<book>
  <chapter id="ch_test">
    <title>Chapter Test</title>

    <para>This is a whitespace test due to &lt;indexterm&gt;,</para>

    <para>0 &lt;indexterm&gt; above this paragraph.</para>

    <para>0 &lt;indexterm&gt; above this paragraph.</para>

    <section id="sctn_1">
      <title>Section 1</title>

      <indexterm>
        <primary>Term 1</primary>

        <secondary>Term 1-1</secondary>
      </indexterm>

      <para>1 &lt;indexterm&gt; above this paragraph.</para>

      <para>0 &lt;indexterm&gt; above this paragraph.</para>

      <indexterm>
        <primary>Term 1</primary>

        <secondary>Term 1-1</secondary>
      </indexterm>

      <para>1 &lt;indexterm&gt; above this paragraph.</para>

    </section>

    <section id="sctn_2">
      <title>Section 2</title>

      <indexterm>
        <primary>Term 2</primary>

        <secondary>Term 2-1</secondary>
      </indexterm>

      <indexterm>
        <primary>Term 2</primary>

        <secondary>Term 2-2</secondary>
      </indexterm>

      <para>2 &lt;indexterm&gt; above this paragraph.</para>

      <indexterm>
        <primary>Term 1-1</primary>
      </indexterm>

      <para>1 &lt;indexterm&gt; above this paragraph.</para>

      <para>0 &lt;indexterm&gt; above this paragraph.</para>

      <indexterm>
        <primary>Term 2</primary>

        <secondary>Term 2-1</secondary>
      </indexterm>

      <indexterm>
        <primary>Term 2</primary>

        <secondary>Term 2-2</secondary>
      </indexterm>

      <para>2 &lt;indexterm&gt; above this paragraph.</para>

    </section>

    <section id="sctn_3">
      <title>Section 3</title>

      <indexterm>
        <primary>Term 3</primary>

        <secondary>Term 3-1</secondary>
      </indexterm>

      <indexterm>
        <primary>Term 3</primary>

        <secondary>Term 3-2</secondary>
      </indexterm>

      <indexterm>
        <primary>Term 3</primary>

        <secondary>Term 3-3</secondary>
      </indexterm>

      <para>3 &lt;indexterm&gt; above this paragraph.</para>

      <indexterm>
        <primary>Term 1-1</primary>
      </indexterm>

      <para>1 &lt;indexterm&gt; above this paragraph.</para>

      <para>0 &lt;indexterm&gt; above this paragraph.</para>

      <indexterm>
        <primary>Term 3</primary>

        <secondary>Term 3-1</secondary>
      </indexterm>

      <indexterm>
        <primary>Term 3</primary>

        <secondary>Term 3-2</secondary>
      </indexterm>

      <indexterm>
        <primary>Term 3</primary>

        <secondary>Term 3-3</secondary>
      </indexterm>

      <para>3 &lt;indexterm&gt; above this paragraph.</para>

    </section>
  </chapter>
</book>

My apologies if this is Apache's FOP
(https://issues.apache.org/bugzilla/show_bug.cgi?id=52526).