There are some people suggested to edit the registry but the proper way to disable CHKDSK from starting up is using the /x switch on chkntfs command in command prompt. The /x switch will exclude a drive from the default boot-time check. If you have drive C: as your hard drive, then the command to disable chkdsk from scanning C: drive would be:

chkntfs /x c:

If you have 2 drive, C and D, you can disable chkdsk with the command below

chkntfs /x c: d: