The System File Checker tool needs to be run as Adminsitrator. If you did not use an Admin account, please try again. You may also want to run SFC in Safe Mode (Restart your Computer, tap F8 until the startup options appear, select Safe Mode).
If no luck with SFC completing, I suggest you run chkdsk. See this tutorial for instructions: Disk Check
Follow with a shutdown/restart and then run the Microsoft Fix it
in both default and aggressive mode to reset the Windows Update components.