I'm documenting RAD 6 issues. Besides keeping RAD up-to-date (and WAS, too), you also need to keep the WAS test servers in RAD up-to-date.
As discussed previously, a test server in RAD is a full WAS server. So to make your testing as accurate as possible, your test server needs to have the same patches as your production server.
There's a document on how to apply WAS server patches to your RAD test server, "Upgrading the WebSphere Test Environment V6 in Rational Application or Web Developer" (Reference #1199423). It explains how to determine what version of WAS your test server is, and how to take WAS patches and apply them to a RAD test server.
(Thanks to Bill for pointing out this document to me.)
Aug 23 Update:
There's also documentation on how to do this in the RAD InfoCenter. See WebSphere Application Server maintenance releases.