We also encounted a similar problem when migrating EJB2.1 to EJB3.0 (and WSAD 5.1.2 -> Eclipse Galileo). Addition of the JBoss.xml to the projects META-INF folder was our solution. We only have use local business interfaces, and the JBoss.xml looks like the following:
<?xml version="1.0" encoding="UTF-8"?>
<jboss xmlns:xalan="http://xml.apache.org/xalan-j/">
<enterprise-beans>
<session>
<ejb-name>TestBean</ejb-name>
<local-jndi-name>ejb/TestBean</local-jndi-name>
</session>
</enterprise-beans>
</jboss>
The <local-jndi-name> can then be used in the InitialContext lookup, without having to use the "<AppName>/BeanName" format that is the default format (JBoss 5.1.0).
Regards,
Greg