If a partition is marked as dirty it will not be cleared.
Type :
fsutil dirty query d:
Volume - d: is Dirty
You can also set the dirty bit if you want by : fsutil dirty set d:
CHKNTFS /X d:
/x = not to check the volume at start-up
chkdsk /f /r d:
You can manually remove the dirty bit :
Download a hdd hex editor : DMDE GUI for Windows
Select Logic/disks volumes, select the volume and press Open volume.
ALT+C = volume cluster selection + ENTER
CTRL+S = Search string --- and paste in the hex part:
03 01 00 00 00 00 00 00 80 00 00 00 18 - no dirty bit
03 01 01 00 00 00 00 00 80 00 00 00 18 - win xp, win 7
03 01 01 01 00 00 00 00 80 00 00 00 18 - win 8
CTRL+E = edit
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