I fixed this in trunk, but not 5_x, so I will fix that now. Not calling "create-thirdparty" at all on a clean would be my first choice also, but the build fails if it can't find libraries.ent (which is generated create-thirdparty) and all the properties it contains. While libraries.ent needs to be present for the clean, it doesn't need to be up to date. So the checkthirdparty is just an optimization so that we don't have to regenerate thirdparty for every clean.
BUILD FAILED ~/work/jboss-5.x/server/build.xml:202: Reference jboss.jboss.bootstrap.classpath not found.
As a workaround:
./build.sh createthirdparty clean main