Next thing I would check is the agent logs after a quarantine attempt.
You can use this test PE to trigger a quarantine event. After the event is complete, open the log file, scroll to the bottom and look for any messages associated with the quarantine attempt.
Just to confirm. When you go to Endpoint Management > Endpoint Administration, select an endpoint that is failing, right-click and select View Endpoint Policy -- can you see the profile with quarantine enabled applied to the specific machine?
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