We are running this as a silent runonce policy Scheduled Task. The batch file runs as the currently logged on user. So how can the job fail because a user is not logged on? Policy will not start until they logon.
Are you sure you only have your policies launching at logon? It is pretty common to have them running at scheduled intervals regardless of whether someone is logged in or not.
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It could be related to the fact the machines that completed the task successfully were the ones with a user "logged in". What if you try to deploy it on machine with no users logged in?