I stopped trying to troubleshoot that problem a year ago. Instead I run a scheduled task every day to delete systems with duplicate hostnames out of the System Tree. When the agent executes a new ASCI, the agent record will be re-created. In my experience, it will be re-created in the location it was deleted from.
When the McAfee Agent is installed onto a system the very first time, a unique identifier is generated and placed into the systems registry.
From the point forward numerous things can occur.
Such as if you use ACCC or software like Deep Freeze that freezes the system environment\desktop. That tends to cause sequence errors since the system may be up for awhile and changes
Failure to clear the GUID from the registry master image before imaging occurs.
You have a couple of queries that contain the word "sequence". Like sequence errors and without sequence errors. Run the query that shows sequence errors and that may begin to get you closer to how many errors are being reported by systems. Make sure to qualify how long the errors have been generated and don't assume that if you see a large number, the errors are current. You can also clear the error count on a particular system and see if the errors begin to generate again within 24 hours. In that case please refer to the ePO guide for how to clear the error, actually clear the registry key, and regenerate a GUID.
Hope that gives you some direction in which to try.