Probably the first thing you should do is make a backup of all your critical data. A full, current, system image would probably be better.
Then I would suggest a couple runs of the native defrag utility on all volumes. Disregard what it says for percentage of fragmentation or last run date.... just run it on all volumes, reboot and run it again.
Then I would run the native Check Disk Utility with the /R (repair) switch, again probably on all volumes but especially on C:
open an elevated command prompt and type
chkdsk C: /R
and hit enter
answer "Y" when prompted
hit enter
type exit
reboot your computer and let it run through all five stages. This will take some time especially on larger drives.
It may provide some insight as to what...