The Apache FOP 1.1 which was released about a month ago has a much stricter policy of checking if references (image references in particular) are made using the proper URI syntax.
For example a Docbook <note> generates an image reference in the XSL-FO file like this:
<fo:external-graphic width="auto" height="auto"
which breaks Apache FOP because the path is a local file system path and not an URL-like path.
We added a bug on the Apache FOP list about this:
but they will not add configuration settings in order to have FOP more lax.