Go to your command prompt>Run as Administrator> type in chkdsk /f /r (space between chkdsk and /f and space between /f and /r).
This will have a 5 step operation. You'll have to reboot for it to start. It'll take some time, so do something while it's doing its thing. It will reair ALL files, etc. That are problematic.
When it's done, it'll reboot into Windows. Hopefully, your problems will have been solved. If not, you may have to do a restore from a backup or a prior point.