Changes in 1.79.1 stylesheets affecting XLink/xref handling?

I recently had to revisit a older project and when now trying to rebuild 
the docs with an updated environment I run into problem.  The docs still 
builds fine with saxon6.5.5 but not with xsltproc both using 1.79.1 
version of the stylesheets.

When I try to regenerate the docs with xsltproc I now get a number of 
errors regarding XLink/xref which the docs makes heavy use of (as well 
as xinclude for modularization). Basically I now get a number of error 
combos:

Error: no ID for constraint linkend: "some-link-that-exists".
XLink to nonexistent id: some-link-that-exists

This makes me think that either:
1) I previously was sloppy and used some syntax that wasn't correct (but 
wasn't flagged as an error and that saxxon still accepts)
2) xsltproc in later version has changed behaviour
3) The stylesheets have a changed behaviour


The way I typically use links is simple:

"Plese see: <xref xlink:href="#section.internal-export-format"/> "

with the corresponding id defined as, in this example a section in 
another file:

"<section xml:id="section.internal-export-format">
<title> some-title </title>
<para> ... </para>
</section>"

Since i really want to use xsltproc and not switch to saxon I was 
wondering if someone can shed some light on the errors of my way and 
what might have changed?