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Yeah, you don't even have to run it in safemode. Just always use this:
chkdsk /r
/r invokes the full 5-step process, but it can't do this on a disk that you're currently on. So it should prompt you to schedule a checkdisk on the next reboot, and you should say yes. The standard 3-step checkdisk process, I've found, is not really too useful.
I don't think you have to use /x unless you want to force disconnect another drive/partition, but you won't be able to do that on the partition you're on obviously.
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