"JBAS015852: Could not index class" error on JBoss EAP 6

Issue

When porting our application from dmServer to JBoss EAP 6, we are getting following error from JDBC driver for DB2

JBAS015852: Could not index class db2-jcc-4-2.8.46.jar/COM/ibm/db2os390/sqlj/custom/DB2SQLJProfile.class at /path/to/jboss/myapp.war/WEB-INF/lib: java.io.IOException: Invalid Magic
at org.jboss.jandex.Indexer.verifyMagic(Indexer.java:389) [jandex-1.0.3.Final-redhat-1.jar:1.0.3.Final-redhat-1]
at org.jboss.jandex.Indexer.index(Indexer.java:630) [jandex-1.0.3.Final-redhat-1.jar:1.0.3.Final-redhat-1]
at org.jboss.as.server.deployment.annotation.ResourceRootIndexer.indexResourceRoot(ResourceRootIndexer.java:78) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
at org.jboss.as.server.deployment.module.ManifestClassPathProcessor.createResourceRoot(ManifestClassPathProcessor.java:266) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
at org.jboss.as.server.deployment.module.ManifestClassPathProcessor.createAdditionalModule(ManifestClassPathProcessor.java:215) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
at org.jboss.as.server.deployment.module.ManifestClassPathProcessor.handlingExistingClassPathEntry(ManifestClassPathProcessor.java:210) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
at org.jboss.as.server.deployment.module.ManifestClassPathProcessor.deploy(ManifestClassPathProcessor.java:172) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
at org.jboss.as.server.deployment.DeploymentUnitPhaseService.start(DeploymentUnitPhaseService.java:116) [jboss-as-server-7.1.2.Final-redhat-1.jar:7.1.2.Final-redhat-1]
at org.jboss.msc.service.ServiceControllerImpl$StartTask.startService(ServiceControllerImpl.java:1811) [jboss-msc-1.0.2.GA-redhat-1.jar:1.0.2.GA-redhat-1]
at org.jboss.msc.service.ServiceControllerImpl$StartTask.run(ServiceControllerImpl.java:1746) [jboss-msc-1.0.2.GA-redhat-1.jar:1.0.2.GA-redhat-1]
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) [rt.jar:1.6.0_20]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) [rt.jar:1.6.0_20]
at java.lang.Thread.run(Thread.java:619) [rt.jar:1.6.0_20]