Chkdsk starts automatically while booting Windows.
Sometimes Check Disk utility (chkdsk) starts automatically on every boot-up even though Windows was shut down properly, because if the Dirty bit of a Disk drive is set, chkdsk scans the dirve for errors even though Disk has no errors.
To solve this problem, go to Start > Run and type cmd and press Enter key. Here at the Command Prompt, type chkntfs /d and press Enter key. This command resets the chkntfs settings to default values and schedules a scan for all Disk drives on next restart. Allow this Disk scan to complete.
Then reboot the system again and check whether chkdsk runs as it would do before. If it does run and scan again, then in Command Prompt type the command chkntfs /x DriveLetter: and press Enter key. Here DriveLetter is the letter of that Disk drive which gets scanned on every boot-up (for example, type chkntfs /x C: if C: drive is scanned every time). This command excludes the specified Disk drive from scanning.
Note that chkntfs also works with FAT32 file system!