I am able to deploy my Session bean successfully in JBOSS under default/deploy folder using the Netbeans IDE. The client for the same could get the reference and invoke the methods.
The deployment for the same deployed jar file when placed under all/deploy goes through fine. But when the client (same client that worked with Netbeans deployement) tries to do a JNDI lookup for the remote interface NamenotFoundException is thrown.
1) Do you start your client from outside Netbeans? Do you have a properties file for the JNDI configuration in place or are the lookup properties directly in your client code? As a NamenotFoundException is thrown it's probably not this problem.
2) Be careful which JNDI lookup name is used to lookup the the interface of your session bean. With Netbeans for example it's a different name when you create an enterprise application as a container for all EJB modules and deploy this enterprise application in contrast to a separate EJB module. It's the best idea to use the JMX console of JBoss to view it's JNDI tree. If you start the JMX console in your browser there should be an MBean "JNDIView" (if I remember it correctly). This gives you a text output of the JNDI data. Search for your interface or bean you're looking for and use this name in your client code. In your client code you have to separate each layer of this JNDI view with a slash in the lookup name.
I hope this may help you. If something is unclear just let me know.