Even with Mojarra 2.1.0? In this case it seems to be a Glassfish integration bug.
I have another idea for a workaround. Perhaps pretty-config.xml is parsed by Mojarra because it matches a pattern like *-config.xml (just like faces-config.xml). In this case you could rename /WEB-INF/pretty-config.xml to something like /WEB-INF/prettyfaces.xml and add the following entry to your web.xml: