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I have a corrupt directory which I cannot delete and when I run CHKDSK in read only mode it finds errors (orphaned files). However since it is on my main (and only) partition I cannot run it with /R to fix the errors. It says it will schedule for a reboot and on my past machines this is exactly what happens when I restart my machine.

However now it seems when I restart it this does not happen and windows boots up on its merry way. Using fsutil I can see the volume dirty bit is still set.

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See this article http://www.winvistaclub.com/t50.html

if it still will not run, run it manually by booting from a W7 install DVD and run chkdsk from the command prompt, once you are at the WinRE command prompt type: chkdsk /r C:

Use this guide to get to the command prompt by booting from the install or system repair disc. http://www.bleepingcomputer.com/tutorials/tutorial147.html

If you do not have a W7 install disc (some PCs come with "recovery" discs and these won't work), see this article on how to make a windows system repair disc http://h10025.www1.hp.com/ewfrf/wc/document?docname=c02058933&cc=us&lc=en&dlc=en

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