Your jibx-run-1.2.1.jar and jibx-extras-1.2.1.jar  are being considered as 
application client deployments. Your jibx-extras-1.2.1.jar consists this 
classpath entry:

anonymous wrote : Class-Path: jibx-run.jar xpp3.jar stax-api.jar wstx-asl.jar

Notice, the jibx-run.jar (which i assume is what you meant by 
jibx-run.jar-1.2.1.jar). So the jibx-run.jar is picked up again through the 
ClassPath entry. There are some known issues with processing ClassPath entries 
in MANIFEST.MF of jars, in AS-5. Try removing the jibx-run.jar entry from the 
Classpath attribute of  jibx-extras-1.2.1.jar:

Class-Path:  xpp3.jar stax-api.jar wstx-asl.jar

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