Where did you "check the settings" to see that it is set to do so?
Describe your current antivirus and anti malware situation: Microsoft Security Essentials (MSE), McAfee, Symantec, Norton, Spybot, AVG, Avira!, avast!. Panda, Trend Micro, CA, Defender, ZoneAlarm, PC Tools, Comodo, etc.
Have you now or ever used any party products on your system where the product description includes one or more of the following descriptive words:
cleaner, mechanic, pit stop, detective, doctor, cure, optimize, inspector, clean up, tune up, speed up, fix up, compact, compress, faster, power, boost, booster, eraser, muncher. one click fix, instant fix, new, intuitive, mistakes, stops freezes, stops crashing,
stops crashes, stops errors, improves, saves you money, risk free, guaranteed or any third party program that has an icon resembling a gear, cog, tool belt, wrench, spanner, screwdriver or swooping arrows?
In addition to the link from TaurArian it would not hurt to run a chkdsk with error correction on the volume.
The drawback with that is it could take many to several hours to complete depending on the size of the volume, the amount of data on the volume, the speed of your system and what the chkdsk finds to do.
If the chkdsk with error correction runs clean, and you still have the problem you can say that you know what the problem isn't (it isn't file system corruption).
Here's how:
https://support.microsoft.com/en-us/kb/2641432