I think that I got it now:
My EJB that are WS endpoints have the following annotation:
@WebContext(authMethod = "BASIC", contextRoot = "webapi", urlPattern = "/ConfigurationVariableWS")
the context root was to override the default context root which is something like ubi-ejb (whatever...)
And in the application context I also had
<module>
<web>
<web-uri>ubi-api.war</web-uri>
<context-root>webapi</context-root>
</web>
</module>
I can't remember exactly why at that time I needed to do that. I hope that I can get rid of this, more tests will tell.
What is not intuitive at all is the error message...
Anyway, my WS seem to deploy correctly now, I'll do some more tests.
I hope that the handler-chain issue will be solved in a future jbossws CXF release as I'd rather use CXF than change jboss default packaging.
Thank you for you time,
Antoine