This is what we did:
1. Issue: metric registration errors and blacklisted
2. We checked the metric limits.
3. We deleted some of the unused applications.
4. We were using Websphere MQ extension.We also added some of the queues to the exclude filters in WMQMonitor in order to reduce the metric footprint.
5. We restarted the MachineAgent and the metrics started reporting both WMQMonitor and ProcessMonitor metrics.