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

Every time I boot my Windows 7 machine, CHKDSK runs.

I have a feeling that the operating system is trying to tell me something, but I don't understand what it is. Any ideas?

Everything works fine so long as I don't reboot.

I treat my computer well, never shutdown with going through Windows "shutdown", etc.

Answer

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.