You may need to tweak the tomcat classpath so that glassfish jars are at the end of tomcat classpath, or only available for a specific webapp. It may have to do with the fact that appserv-rt.jar is alphabetically before other tomcat jars. If it's tomcat 5, you can try putting it in shared/lib instead of common/lib, or packaged it inside the war.
The last resort, you can delete appserv-rt.jar!jndi.properties when using it in tomcat.
-cheng
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