I ran the migration tool ( in the GUI mode) against a WebSphere 5.x ear file and it migrated it successfully. I did set the three env variables JAVA_HOME, ASMT_HOME and J2EE_HOME as described in the http://wiki.glassfish.java.net/Wiki.jsp?page=M2GInstSetup and ran the tool.
The migration tool uses JAXB (there is a version bundled internally) but you might be picking up a different version of JAXB based on your configuration.
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