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If you're seeing that error message on the clients, then that means that the inventory scanner bit cannot talk to the inventory service. Are you seeing this on the client or in the console? If you're seeing this on the console side when doing a right-click inventory scan, then it may be that we are having trouble talking to that machine correctly for that particular task. If it's a right click option, are you able to right-click and perform security scans on those machines as well?
The inventory service on the core is know to hang at time, sometimes if you check the status it will look like it is running, but it is really hung, you can restart the service or reboot the core.
Tyr one or both