Chkdskruns in Windows as a small box or in a DOS box within Windows, or in the Recovery consoleAutochkruns in the blue boot screen and does the same thing that chkdsk does.
Autochkdoes essentially the same thing asChkdskbut will only run during bootup (but during bootup it will only run if the system detects a cold boot or power off).
social.msdn.microsoft.com/Forums/en/embeddedwindowseefs/thread/d90a4d12-6050-4c26-9d6b-c10d3a4ca2c6