Chkdsk Running Everytime At Startup

Method 1:

1. Click on the Start menu and open the Run dialog.
2. Type "cmd" (without quotes) and click OK.
3. Next, type "fsutil dirty query drive letter:" (without quotes)
4. If the message indicates that the volume is dirty, go to step 5.
5. Next, type "chkdsk /f /x"

If you get this, answer YES.

Chkdsk cannot run because the volume is in use by another
process. Would you like to schedule this volume to be
checked the next time the system restarts?

6. After that finishes, repeat step 3.
7. If the volume is no longer dirty, reboot and chkdsk should not reappear.

Method 2: Editing the Registry

1. Go to Start ,Run and type in regedit.
2. Navigate to the HKEY_LOCAL_MACHINE , then go to the following subkey:
\SYSTEM\CurrentControlSet\Control\Session Manager
3. Open the BootExecute entry.

The default value is:
BootExecute: REG_MULTI_SZ: autocheck autochk *

4. Modify this registry entry to autocheck autochk /k:drive letter *

Note is the drive that chkdsk keeps checking

Source: Microsoft.com, Forums.techguy.org