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I used to get the same problem with ePO 3.x but not seen it with 4.x yet.
I just used to run the duplicate systems report, order by machine name and then delete the machine that either doesnt have a last checked in time, or has the oldest checked in time
Ok, I think the issue might have been misreported due to familiarity with the last problems, but the end result is a bunch of machines have been cloned after having had McAfee setup, so they all have the same GUID! This is definitely a concrete problem.
Too many new variables at once going on here, but that seems to be the root cause of our strange behavior. Hopefully dealing with that will clear things up.