The problem is in using migration tool with Java SE 6 (which includes JAXB 2.x). So if you are using Java EE + JDK bundle from
http://java.sun.com/javaee/downloads/index.jsp (as you seem to be based on your description), this will use JDK 6 and you will run into this problem. I will look into this issue further.
In the meantime, the workaround is to use Migration Tool with GlassFish + Java SE 5 (JDK) i.e.
<ol>
<li> download GlassFish distribution without Java SE bundled and Java SE 5 separately and set J2EE_HOME and JAVA_HOME accordingly.
<li> if you have already downloaded Java EE + JDK bundle from
http://java.sun.com/javaee/downloads/index.jsp , then download Java SE 5 (JDK) and set JAVA_HOME accordingly. This seems to override the JDK 6 installed with Java EE + JDK bundle. I verified Migration Tool runs successfully but I don't know what if any are the problems with this approach.
</ol>
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