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Assuming that the custom metrics are generated by a Machine Agent extension, the first place to look is the machine agent log file, which is in $MACHINE_AGENT_HOME/logs/.
The log file will indicate that the extension was enabled, and executed, and if the resulting metrics were registed in the Controller or not.
If you don't see the issue there, you may need to enable debug logging for that machine agent.
Brian Wheeldon, Solution Engineer, NYC