using FOP to apply the DocBook XSL stylesheet as well as
running the FO processor? If so, I would suggest separating
those steps by running saxon 6.5 to apply the DocBook
stylesheet to your XML document and generate a .fo file, and
then use FOP 1.1 and FOP 2.3 to process the .fo file to PDF,
and compare results. That will sort out if it is the XSLT
front end or the FO backend that makes the difference.