Neither the HE version of Saxon 9.5 (there is no 9.6 yet) nor msxsl supports the exsl:node-set()
extension (which is required when removing the namespace). Saxon 9 is an XSLT 2.0 processor which basically means that this extension function is not needed (see also http://www.saxonica.com/documentation/html/extensions/functions/exslt.html). For msxsl, you would need an additional download (see http://www.xml.com/pub/a/2003/08/06/exslt.html).
It should work with Saxon 6.5.5 or xsltproc (XSLT 1.0 processors).
From the error message I see that you are using the non-namespace-aware stylesheets. Since this is about processing DocBook 5, I advice you to switch to the namespace-aware stylesheets (docbook-xsl-ns, available from http://sourceforge.net/projects/docbook/files/docbook-xsl-ns/). Then there will be no need for any namespace-stripping.
You also mention using xi:include
. Any problems with XInclude are probably unrelated to the namespace-stripping issue. I am not sure what you mean by "this" when you say "the windows version does not support this".
See also: