Replying to myself:

The problem was that I overlooked a small detail when resolving a conflict after the update:

In trunk:

<map:serializer name="fo2pdf" src="org.apache.cocoon.blocks.fop.FOPNGSerializer" mime- type="application/pdf" />

I had:

<map:serializer name="fo2pdf" src="org.apache.cocoon.serialization.FOPSerializer" mime- type="application/pdf"> <user-config>/Users/sjur/gtsvn/xtdoc/sd/src/documentation/ resources/fonts/config.xml</user-config>
       </map:serializer>

Note the @src - it had changed without me noticing it, and I just kept my old @src. My bad - apologies for the noise.

Best regards,
Sjur