Resolution:
Hawk HMA must be run by the local system account in order to see the processes started as NT service or other system processes. Granting a user account with local system Administrator privilege is not enough. This seems to be a NT OS limitation, not TIBCO Hawk limitation.

In 5.1 TRA/Administrator release, the domain Hawk agent and HMA are combined as one NT service. So you have to configure the domain Hawk agent to be run by the local system Admin account in order to see all processes running on the local machine.