Solved it - should have added:

else if (args[i].equals("-fontBaseDir")) {
                                log.info("Setting extended property 
-fontBaseDir");
                                if ((i + 1 == args.length)
                    || (args[i + 1].charAt(0) == '-')) {
                                        throw new FOPException("if you use 
'-fontBaseDir', you must
specify the path to the fonts directory");
                                } else {
                                        ((java.util.HashMap) 
((java.util.HashMap)
org.apache.fop.configuration.Configuration.getConfiguration()).get("standard")).put("fontBaseDir",
(args[i + 1]));
                                        i++;
                                }
                                
                    }

instead of the chunk of code previously posted. It works now.

-- 
Why?
Because YES!

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