Why does CHKDSK run everytime I boot my Windows 7 machine?

"The proper way to stop chkdsk from running on startup is to use chkntfs:

chkntfs /x c:

Where c: is the drive you're excluding from the disk check. You can use multiple drives as arguments like so:

chkntfs /x c: d:

Explanation of the various switches:

C:\Documents and Settings\Administrator>chkntfs /?
Displays or modifies the checking of disk at boot time.

CHKNTFS volume [...]
CHKNTFS /D
CHKNTFS /T[:time]
CHKNTFS /X volume [...]
CHKNTFS /C volume [...]

volume Specifies the drive letter (followed by a colon),
mount point, or volume name.
/D Restores the machine to the default behavior; all drives are
checked at boot time and chkdsk is run on those that are
dirty.
/T:time Changes the AUTOCHK initiation countdown time to the
specified amount of time in seconds. If time is not
specified, displays the current setting.
/X Excludes a drive from the default boot-time check. Excluded
drives are not accumulated between command invocations.
/C Schedules a drive to be checked at boot time; chkdsk will run
if the drive is dirty.

If no switches are specified, CHKNTFS will display if the specified drive is
dirty or scheduled to be checked on next reboot."

"John T beat me to the command, but in addition, it is worth noting that this is controlled through ""Boot Execute"" in Microsoft/Sysinternals Autoruns, you can delete entries there, or go to the registry key they are stored in:

HKEY_LOCAL_MACHINE\SYSTEM\CURRENTCONTROLSET\CONTROL\Session Manager

Autochk.exe seems to be there by default - it is just the c: (and any additional drive) parts that you need to delete. The default value for the registry key (incase you delete something by accident) is autocheck autochk *."