Thanks a lot Kohsuke.
When you deploy a webapplication using IPlanet UI, IPlanet doesn't clean up the webapplication lib directory. IPlanet puts all the new libraries in the WEB-inf\lib folder and overrides any libraries with the same file name. We were upgrading to JAXB-1.0 and the old beta library was already there in WEB-INF\lib folder.
I have to do a hard-delete on the webapplication directory.
Thank you
Sree Pillai