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I installed Windows 8 (retail) on a new drive with my Windows 7 drive unplugged. So each Windows has no idea about the other one and I use the BIOS boot options to select which drive hence OS to boot into.

Now whenever I boot into Windows 8 then boot into Windows 7, Windows 7 runs chkdisk presumably because Windows 8 messed with it.

Is there anyway to stop this? (In hindsight I should have installed Windows 8 with Windows 7 drive plugged in so I could use the Windows dual boot options).

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related superuser.com/questions/464259/… –  bytebuster Sep 30 '12 at 2:57

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First off, you may use CHKNTFS.EXE. Download link. An excerpt from its docs:

The Chkntfs.exe utility has been developed by Microsoft [...]. It is designed to disable the automatic running of chkdsk on specific volumes, when Windows restarts from an improper shutdown. Chkntfs can also be used to unschedule a chkdsk if chkdsk /f was used to schedule a chkdsk on an active volume on the next system restart.

Yet another solution is checking whether Windows 8 is indeed shutting down, not hybernating to a "hybrid boot". This thread helped me for CTP, but frankly I have not tested it against the retail version.

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Thanks. My concern with disabling chkdsk is should there be genuine reason for it running it will not! Whether Windows 8 is shutting down or not I would hope I could leave it to do its thing - if it does hybird boot by default I would like to have my cake and eat it. –  markmnl Oct 2 '12 at 5:23
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Unless shut down properly, Windows marks volumes with a "dirty" flag. With hybrid boot, Windows 8 leaves this flag. If you start into Windows 7, it sees dirty flag, but it does not know which system has put this flag; it simply thinks it has not been shut down properly and runs CHKDSK. The only way to avoid running disk check is proper shutdown of all systems you have. Or disabling the check at your own risk. –  bytebuster Oct 2 '12 at 10:20
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thanks. btw: I re-installed Windows 8 with my Windows 7 drive plugged in so I now get the Windows 8 dual boot options to select which OS I want to boot into. –  markmnl Oct 4 '12 at 1:55

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