It seems that table of contents is not generated for a reference as the toplevel element in the FO stylesheets. Using a toplevel element other than reference (book or section for instance) containing the reference will generate the toc's containing the reference contents and the HTML stylesheets will generate the toc's for a toplevel reference element. It looks like the fo stylesheets are missing a call to the TOC templates, but I can not follow the structure well enough to be sure.
A sample document is included. There should be a TOC containing the two refentries, but a TOC will not be generated for any permutation of the generate.toc parameter. Here is the document:
<reference xmlns="http://docbook.org/ns/docbook" version="5.0" xml:lang="en" xmlns:xi="http://www.w3.org/2001/XInclude">
<title>Test Reference</title>
<refentry>
<refmeta>
<refentrytitle>Test Refentry1</refentrytitle>
</refmeta>
<refnamediv>
<refname>Test</refname>
</refnamediv>
<refsection>
<para>Testing</para>
</refsection>
</refentry>
<refentry>
<refmeta>
<refentrytitle>Test Refentry2</refentrytitle>
</refmeta>
<refnamediv>
<refname>Test</refname>
</refnamediv>
<refsection>
<para>Testing</para>
</refsection>
</refentry>
</reference>
I checked in a fix for this problem. Thanks for the report.