I'm not a windows person, so I don't know if they have a concept like suid (where the program is always run with another set of permissions). But they do have schedulers and the like. If the program is run through a scheduler, there's a reasonable chance that it's running with permissions other than your login. I'd suggest you talk to your system administrator. If you are the system administrator, I'd suggest that you take a look at the preferences and settings in whatever you're using to trigger the script.
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