Please check the AutoProbe.log for the VM where the metrics are not showing:
a) Check the pbd file is listed in the AutoProbe.log
b) Check the classes instrumented in custom.pbd are listed in the AutoProbe.log (Second part of the AutoProbe.log)
c) Check the classes / methods from custom.pbd if the methods are listed as instrumented with the tracer
d) Metrics are still not showing
Error analysis:
a) fails => The pbd file was not accessible, not there or the restart didn't happen. Maybe wrong IntroscopeAgent.profile ?
b) fails => The code which is targeted on "custom.pbd" was not (yet) executed / not loaded
c) fails => either the class doesn't declare the method or it's declared in a super class and thus the byte code injection failed.
d) fails => Check whether you run on the Agent into a metric clamp situration
Small side node. In case it's on WebSphere's with Class Caching enabled, strange things can happen with Byte Code Instrumentation. Mostly once a change is done on injection, it is recommend to clear the class cache and restart all nodes.