Silly question but have you ensured that the correct policy is applied to the Workstation?
Its not a silly question at all. I've actually verified this on a dozen or so machines and I'm completely confident that this policy has been applied for ages.
When you say the "Stop McAfee Processes" option in AP, do you mean the "Prevent termination of McAfee processes"?
Because the behavior should be as you were expecting.
If you don't see the policy in the local client you may have discovered a policy corruption problem, if not a server-to-client communication problem.
Best case, it may be a UI only problem, but it would require some investigative work to establish that. I suggest contacting Support.
We've been seeing a similar problem.
Here it started shortly after we deployed Patch 5. After deploying Patch 5, a lot of our systems didn't apply our policies but reverted to McAfee default policies instead.
I believe it had something to do with the new VSE extensions.
Deploying Patch 6 a few days later helped a bit but not for all systems.
See if this KB article applies to you : https://kc.mcafee.com/agent/index?id=KB84913 (Access Protection Policy content no longer displays in ePolicy Orchestrator after deploying the VirusScan Enterprise 8.8 Patch 5 or Patch 6 extension)
There are other KB articles which might apply.
VirusScan Enterprise 8.8 Patch 5 Known Issues https://kc.mcafee.com/agent/index?page=content&id=KB81381
I know you mentioned Patch 6, but this might help.
Good luck and keep us informed
I'm leaning toward support too. I just thought I would verify that this is not normal behavior first.