Files not updating in circumstances after update

Do you have Malwarebytes Anti-Malware full version (paid) or the free one? The free version, despite it is loaded with windows, is only for on demand scans and It doesn't protect your computer. Scan the computer with it.

Did you try to roll back with System Restore?

I've scanned with free Malwarebytes, but there are no threats. I'll try a System Restore, and see if that helps.
EDIT: Nope, System Restore hasn't worked for me. There wasn't a System Restore point for the update, so I just did the last one before the update (I can't remember the exact day I did the update). I'm still having the same problem.

Open a CMD window and type:
chkdsk c: /f
It will ask if you want to Schedule a disk check for next boot =Yes
Reboot. Pay attention on the results, specially bad blocks or bad clusters.

After reboot, do a System File Check. Open a CMD window and type:
sfc /scannow

chkdsk found no problems with the disk, but sfc crashes about 14% in, with a "Windows Resource Protection" could not perform the requested operation".

Boot from the Win 7 installation disk, go to repair and launch a CMD window and type:
sfc /scannow

I unfortunately do not have my disk handy, is there another way I could do it?

Try safe boot (F8 during POST).

I tried booting in safe mode with command prompt, still got the same message when I tried to scan.

You must look for your Win 7 installation disk.