The prefix customization copied the chapter template from
the 1.60 stylesheets. That template put the chapter
id on the fo:page-sequence element, which FOP did not
understand, so it could not find that id to assign a
page number in the TOC. Version 1.61 of the stylesheets
moved the chapter id to the first fo:block in the chapter,
fixing the missing page number in the TOC.
See the match="chapter" template in fo/component.xsl
in the 1.62.4 stylesheets to see how the id location
was changed. So the customization file needs to
be updated.