The problem: When I generate the PDF with the JSP my fo:basic-links don't make it into the PDF. If I dump the FO DOM tree to a file and use fop from the commandline the links are present in the PDF.
Are you, by any chance, using disable-output-escaping somewhere?
Yes, but somewhere else in the stylesheet producing the fo document.
Behaviour does not change if I comment out the two lines (that do not work with embedded fop either).