Every time when you boot your PC, CHKDSK runs for particular drives(c:,d:,e:,f: ...). If you let it run completely and then immediately or later restart PC, CHKDSK runs again. The cause is your drive is dirty..
The fix for the above solution is simple. Just follow step below :
1) Click on START --> RUN.
2) In Run dialog box type cmd and Press Enter.
3) In cmd prompt type fsutil dirty query d: (where d: is dirty drive).
4) It will return message where Volume d: IS Dirty or NOT Dirty.
5) If the Volume is Dirty then type chkdsk d: /f /x.
6) After that finishes repeat STEP 3.
7) If it will show NOT Dirty then reboot your system and you wont see CHKDSK again..