You don't have an endorsed standards directory? Then make one. Unfortunately the link mentioned in the stack trace seems to be broken at the moment, while Oracle moves all the Java pages from sun.com to oracle.com. (but you did try to follow it, didn't you?) So here's a link to someone else who explains it for you, which I found after a couple of minutes googling: http://futuretask.blogspot.com/2005/01/java-tip-4-endorsed-standards-override.html.
subject: java.lang.LinkageError: JAXB 2.0 API is being loaded from the bootstrap classloader