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It looks to me that you are using a logon script to run administrative tasks on machines. I firmly believe that logon scripts should only be used for user based changes.
If that is the case, may I suggest using a group policy start-up script (which runs as SYSTEM) for machine based changes?
What we do in our environment is to have a group policy startup script create a scheduled task with SYSTEM privileges on all our machines. That scheduled task calls a KiX script in a sub folder the sysvol share on the domain controllers that does our machine based changes.
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