When Windows didnot not shut down correctly, it will perform an AutoCheck
using CHKDSK on the next restart.

AutoCheck is executed after a short time delay. AutoCheck can be
disabled or delayed by tweaking a few Registry settings.
Run ‘Regedit’ from ‘Start Menu|Run...’
Create a new DWORD value, or
modify the existing value, called
“AutoChkTimeOut” and set it according
to the value data below.
Value Name: AutoChkTimeOut.
Data Type: REG_DWORD (DWORD Value).
Value Data: Time in Seconds or 0 to disable
(default = 10).
Exit your registry, you may need to
restart or log out of Windows for the
change to take effect.