I have found a problem with the version of Tomcat (5.5.9) bundled with JBoss 4.0.2 and above.

Any context configuration in the 'jbossweb-tomcat55.sar/context.xml' and 'WEB-INF/context.xml' is processed twice when a web application is deployed.

I have raised the issue at Apache and a fix has been applied to their CVS that will be in the 5.5.13 release.

http://issues.apache.org/bugzilla/show_bug.cgi?id=36802

Do you want an issue rasing in Jira to keep track of this or is a different process followed to keep up to date with the Tomcat versions?