If a jboss-app.xml is packaged in a jar file and specifies a loader repository as shown below, then JBoss is isolating the ejb. The jboss-app.xml should only be valid for an ear file. jboss.xml should be used for an ejb. JBoss should ignore the jboss-app.xml and log a warning or exception that jboss-app.xml shouldn't be in a jar file.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE jboss-app PUBLIC "-//JBoss//DTD J2EE Application 1.4//EN"
"http://www.jboss.org/j2ee/dtd/jboss-app_4_0.dtd">
<jboss-app>
<loader-repository>
com.jboss.examples:loader=example-ejb.jar
<loader-repository-config>java2ParentDelegation=false</loader-repository-config>
</loader-repository>
</jboss-app>