As stated in the knowledge base (60533), Techinal support team will attempt to answer basic questions regarding SaaS Endpoint Protection issues that occur in a virtual environment. However, for full support, you will need to reproduce the issues in a non-virtual environment(Physical Machines).
Since you have mentioned that the updates are fine with physical servers, hopefully you may need to wait untill virtual environment is fully supported by McAfee SaaS End Point Protection Service.
Per your statement, "....you may need to wait until virtual environment is fully supported by McAfee SaaS End Point Protection Service."
Can you follow up please and ensure that everyone is updated on McAfee's progress on this matter. It appears there are more people (even a year later) that are experiencing issues.
I just found this McAfee document that is very recent: https://kc.mcafee.com/corporate/index?page=content&id=KB60533#Virtual
It appears that virtual environments are still NOT supported. I find this disturbing as all companies have virtualized environments in one way or another now days.
McAfee needs to step it up and get a solution that is supported. Frankly, if I would have known this a few months ago, that would have been a deal breaker to find a supported solution else where.
Virtualization is here to stay... Please update your products in a timely manner to support same.