Was having the same issue with 10.2. Just got off the phone with Esri and it appears this is a known issue. The technician said that the server gets overloaded on reboot and applies security to the System directory. The fix is easy: - log in to ArcGIS Server Manager - Click on System folder. Is the lock icon locked? If so, click on it and make sure it is set to Public and hit SAVE. [ATTACH=CONFIG]30232[/ATTACH]
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