I am having troubles migrating from OC4J 10.1.2.3 to 10.1.3.1.4. The problem is for applications that have multiple EJBs (all are 2.1, no EJB 3.0). Jdeveloper will take the default ejb-jar.xml (the one required for Jdeveloper to run it on its stand-alone OC4J instance) and package it into each EJB JAR module NO MATTER what. This results in the app server drilling into each EJB JAR module when deploying, and find the same ejb-jar.xml file N times (where N = number of EJB Modules). This results in duplicate EJB references and will break any JNDI lookups such as: "java:comp/env/ejb/EJBName". Thus deploying an app that has 3 EJBs, EJB1, EJB2 and EJB3 causes the app server to register 9 EJBs instead of 3. I need a best practices way, but in between the way 10.1.3.4 and JDeveloper are acting the situation is rather dire...
Side note: They will work if the web app's JNDI look-up code is refractored to just "ejb/EJBName". This is not desirable though.