Sometimes you have to run CheckDisk from Safe mode as win often gets in its own way for low-level functions like that. There is also a way to set up CheckDisk to run during boot rather than in Safe mode which runs before a lot of Win is loaded up, but I've forgotten how to do that. As suggested above, use your drive mfr's diagnostic disk to scan for hardware errors as that boots separately so Win can't get in the way. There are also third party scanDisk type programs that boot separately so win won't get in the way.
Perhaps the best disk hardware checker is SpinRite, but it can take forever on a deep level on today's huge drives. It's lowest level of testing approximates the mfr's integrity check. But S-R isn't cheap and I don't think it checks for file structure integrity like scanDisk or checkDisk does. So you'll need another program to do that as well.
http://www.majorgeeks.com is where I go to find free diagnostic tools.
.bh.