When a new Introscope Java agent is deployed to a Tomcat app server from the "allappserver" tarball package and Tomcat is configured to use the agent and to report JMX data, then JMX metric data is not visible within the Introscope Investigator. This is true regardless of the PBD selection (typical versus full) with agent-side JMX functions fully enabled (introscope.agent.jmx.enable=true and no filter specified in introscope.agent.jmx.name.filter).
The "allappserver" flavor of the Introscope agent tarball is, as the name implies, all-encompassing to include configurations suitable for the many application servers that the agent supports. It is shipped with a directory structure and file content suitable for use on many different app servers. One side-effect of this is that the one extension needed for JMX metric functionality is not in the directory location that the Tomcat agent requires: WebAppSupport.jar. This jar is shipped in the "allappserver" tarball within the wily/common/ directory. However for JMX metrics from a Tomcat agent to report to Introscope, this jar must reside within the wily/core/ext/ directory instead.