Источник - http://serverfault.com/questions/534891/run-sfc-scannow-as-administrator-but-i-am-administrator

При запуске команды sfc /scannow появляется ошибка You must be an administrator running a console session in order to use the Windows File Checker utility

Решение

mstsc /console /admin

You need to choose Run as on CMD and type in login and password of Administrator. Then you can run the command. You need to be logged in RDP in CONSOLE mode (/console or /admin switch depending on RDP version). Then it will work.