my experience is when an ntfs partition starts giving chkdks errors its a sign of doom. its obviously found file system errors, and I don't think they always get properly fixed.
the simple fixable errors get fixed without any intervention by chdksk, as the ntfs maintains a special file to always be able to restore the file system to the previous good state if power is lost during a file update.
if you have two drives its a good idea to have both with a bootable OS installed, you can then boot from one drive and repair the other from within windows by locking the drive then you can run chkdsk or other utility on that drive as it isn't used by the OS, unless you've set it up awkwardly. this means you can more easily see whats going on than the boot time check.
also its a good idea to run a low level non destructive read test usually the manufacturers provide a floppy disk based program, this makes sure there are no hard drive probs. any errors at all spell trouble.
if you have any disk doctor type tools these can cause problems in themselves too, boot time defragmentation is probably the most dodgy.
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