How are you entering the machine name into the machine group? It will base the scan upon how you enter it. It may help to enter the FQDN instead of the short name. Also, you could enter the machine by IP address and it should help workaround using the name.
We want to deploy updates using "Hosted Virtual Machines". Entering the IP address manually on a high number of VMs are not preferable.
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You could take a look in the following Help document in Protect to see if there is anything that helps you:
Otherwise I think it might be best to open a case directly with support so we can get logs and work more closely on this issue with you.