Here's a follow up on what I found out about this problem. First, I would like to restate my problem. This happens in Tomcat Embedded mode. The version of Axis is 1.2, and Tomcat is 5.028 and 5.5.4. When I stop() and start() the axis webapp, the AdminServlet causes this problem. The webapp actually works, with the happy axis page showing no error. However, when clicking on "View" the list of deployed Web services, the error also show up. Disable AdminServlet would make the problem go away. When using the embedded version, if calling stop() on both the web context and the Tomcat Embedded's instance, then re-create and start them all, the AxisServlet will also generate this error. There is an existing bug report at apache on this:
http://issues.apache.org/bugzilla/show_bug.cgi?id=27371
Please also note that using the standalone version and the tomcat's manager, calling stop() and start() on the axis web app works fine without any problem.