> <map:serializer name="pdf" mime-type="application/pdf"
> src="org.apache.cocoon.serialization.FOPSerializer">
>    <user-config src="webapps/ROOT/doc/fop/config.xml"/>
> </map:serializer>

you should try <user-config
src="context://webapps/ROOT/doc/fop/config.xml"/>.

On the other side the problem can be bug in batik which occurs as a NPE.
When using internal url targets in your fo:instream-foreign-object this
problem is present. This bug is fixed in current batik version 1.5 beta4.
This solved some of my problem's i had with current HEAD (cocoon-2.1).

hth,
Frank



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