Hi, I encounter the same matter.
I have around 200 computer not checking in anymore.
I tried installing agent V7 on a new computer => not reporting
Running agent upgrade task from ESMC (6.5 to 7) = most of the time the agent gets upgraded on client station but as it doesn't report anymore after upgrade well ESMC says the client has an outdated agent....
I guess we have to wait ?
Please Help !