The presence of a META-INF/ejb-jar.xml file that is not properly namespaced, for example...

<ejb-jar>
</ejb-jar>

...instead of...

<ejb-jar version="3.0"
xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/ejb-jar_3_0.xsd">
</ejb-jar>

...stops ALL of the annotation-based metadata processing. Every session bean in the JAR reports with the JBMETA-4 warning, and therefore none of them get registered with JNDI. This is much worse than simply ignoring the ejb-jar.xml altogether, as is arguably acceptable as it isn't namespaced.

An un-namespaced ejb-jar.xml is not uncommon. Many examples, including this one from the JBoss documentation...

http://docs.jboss.org/ejb3/app-server/reference/build/reference/en/html/partial_deployment_descriptors.html

...leave off the namespace, so for JBoss to fail without warning seems a little harsh. Leaving off the namespace worked fine in JBoss 4.2.3.GA.