EPUB conversion to PDF toc fails to navigate

99% of the EPUBs I convert to PDF have a working toc but I have one EPUB that the PDF toc fails to navigate. The EPUB toc work in calibre but not in the created PDF. The only odd thing I noticed is the the toc.ncx is in the root of the EPUB but the html pages are in the 'text' directory.

Any suggestions how to get the pdf toc to work?
Thanks