I am having _exactly_ the same problem using dynamic class loading in an attempt to access Jini services.
Curiously, neither of us are attempting to access resources via JNDI so Catalina must be confused. Is this a bug with JBoss/Tomcat integration?
Try using a more recent bundle of jboss/tomcat and report the full exception if this persists. The symptons indicate a conflict with handling of the jndi url prefix as a jndi protocol handler vs a url protocol handler.
This issue does appear to be resolved in the JBoss3.2.3/Tomcat4.1.29 bundle.
If anyone knows the precise location of the fix, however, I would be very grateful for a pointer. It is no trivial matter for my organisation to upgrade our production systems but I could get an updated JAR past the admins.