Would definitely recommend using 6.0.1 manager and 6.0.1 agent if at all possible, or using the 6.0.0 hotfixed agent in the meantime if it's the NT AUTHORITY\SYSTEM issue you're working around. I can't guarantee it will fix the issue, but due to the way the console communicates to the agent via the manager, it will likely have an impact.
Are you seeing this on all 6.0.1 agents or any 6.0.0 agents, too (you mentioned you checked others, are they all 6.0.1/mismatched)?