Check Disk runs on every boot: Note - I have seen this happen when Windows File Protection has either been disabled or not allowed to run upon canceling the bootup Check Disk
Go to Start/Run/CMD and type in: fsutil dirty query c:(Modify the drive letter accordingly)
If it comes back as dirty, it hasn't cleared. For more information go to Start/Run/CMD and type in: CHKNTFS /?
Option: From a command prompt type chkntfs /D and then reboot, a chkdsk should run but not again on next boot
This edit does not work for all users, circumstances depending:
Disable or Enable CheckDisk Upon Boot :
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon]"SFCScan"=dword:0000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager]"AutoChkTimeOut"=dword:0000000a
Copy above text and paste in notepad .You just save them with a .reg extension.
Right click on this file and click on merge.
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