What do you mean by " the configuration for jboss is created without JAX WS."? How can you tell? What was it that you expected but was missing?
I have create JAX-WS POJO web services and there is little difference between the resulting WAR and that of a web application.
Finally, this could be an Eclipse packaging issue, in which case you should ask this in an Eclipse forum (or on the JBoss Tools forum if you are using JBoss Tools).