I don't know if I can help, but I have an example working. Here is my web-service.xml:

<deployment name="OrderService"
targetNamespace="http://org.jboss.docs.cmp2.commerce/OrderManager"
xmlns:OrderManager="http://org.jboss.docs.cmp2.commerce/OrderManager"
xmlns="http://xml.apache.org/axis/wsdd/"
xmlns:jbnet="http://org.jboss.docs.cmp2.commerce/server"
xmlns:java="http://xml.apache.org/axis/wsdd/providers/java">

<!-- this is an extension to the Axis deployment descriptor which allows to
specify the naming environment for the deployed ws logic -->

<!-- OrderManager reference -->
<ejb-ref>
<ejb-ref-name>ejb/OrderManager</ejb-ref-name>
<ejb-ref-type>Session</ejb-ref-type>
org.jboss.docs.cmp2.commerce.OrderManagerHome
org.jboss.docs.cmp2.commerce.OrderManager
<ejb-link>OrderManagerEJB</ejb-link>
</ejb-ref>



<!-- the final jndi name that this provider sits upon-->




This is with JBOSS 3.0.0. The beanJndiName "commerce/OrderManager" is the same as the jndiName in my jboss.xml

<ejb-name>OrderManagerEJB</ejb-name>
<jndi-name>commerce/OrderManager</jndi-name>


My application.xml looks like this:


<display-name>commerce</display-name>

commerce.jar


OrderService.wsr



and my OrderService.wsr has the web-service.xml, as well as my ejb's home and remote interface classes.

OrderManager is a stateless session bean that provides a facade to the commerce cmp2 example. (I think from reading the project page for Jboss.NET that its EJB support is limited to session beans).

By the way I seem to remember getting NameNotFoundExceptions when I tried to use java:comp/env/ejb/OrderManagerEJB, but you appear to be using the global jndi name that is successful from you RMI client.

Hope this helps.