I ran into this issue recently. Running "SFC /scannow" does nothing. In order to fix it, I had to manually reclaim ownership of my user's library folder. To do this, you need to navigate to:
Then right-click the "Libraries" folder, and choose Properties -> Security -> Advanced -> Owner -> Edit.
Now temporarily assign ownership of the folder to another user or group on your computer. The "Administrators" group will work just fine. Apply the changes and exit out of your properties box(es).
Finally, repeat the steps above, and this time assign yourself back as the owner of the folder. Apply the changes, and everything should be fix. Or at least, it was in my case.