Greets,
Nico Van Cleemput
Ghent University

This does look as if the JDK 5 processor had a pretty nasty bug.

The code seems to be written on the assumption that

key('vertex',@from)

will select data from EMBEDDING.XML; but the context node at the time is in
GRAPH.XML, so that is where the key should search. I'm afraid the fix for
this in XSLT 1.0 is tedious: my advice, since you're switching processors
anyway, would be to switch to XSLT 2.0 and Saxon, where you can write

key('vertex', @from, $embedding)

having declared the global variable:

<xsl:variable name="embedding" select="/"/>

Michael Kay
http://www.saxonica.com/