Have you tried sfc scan during boot?:
http://www.sevenforums.com/tutorials/139810-sfc-scannow-run-command-prompt-boot.html -
tutorial created by Bare Foot Kid
Why are you attempting a scan, is it just in case or are you experiencing problems. If you are, please let me know in detailed form what is going on.
Also, let me know how this works out for you. If not, Ziggy above probably has the best advice you could use at this point.