When using WSIT with JDK6 (initial release and updates 1 and 2), there are conflicting versions of the JAX-WS APIs. Specifically, JDK6 ships with JAX-WS 2.0 APIs and WSIT ships with JAX-WS 2.1 APIs.
Previously WSIT didn't support installing to Tomcat 6. A problem mainly caused by a directory, shared/lib, that is no longer part of the default Tomcat install image. A manual workaround for this was described by Arun Gupta in one of his blog entries, here.