Not too much detail in your post but in general, the bad sectors don't have to be in C, they can be in the smaller partitions or any other included in your job.
The small partitions often do not have drive letters assigned so to chkdsk them you have to assign a letter which can be done using Window's Diskpart via a Terminal. Right-click on the blue Windows icon and select Terminal (admin) - admin just in case you need the admin permissions. You can/should remove the letter after checking.
Did you use chkdsk [partition letter] /r or just /f? /f checks the file clusters in use and you would think that would be adequate, however, /r checks the whole partition and can sometimes pickup bad clusters causing a problem. Unfortunately, for a large partition /r can take a long time.
The small partitions often do not have drive letters assigned so to chkdsk them you have to assign a letter which can be done using Window's Diskpart via a Terminal. Right-click on the blue Windows icon and select Terminal (admin) - admin just in case you need the admin permissions. You can/should remove the letter after checking.
Did you use chkdsk [partition letter] /r or just /f? /f checks the file clusters in use and you would think that would be adequate, however, /r checks the whole partition and can sometimes pickup bad clusters causing a problem. Unfortunately, for a large partition /r can take a long time.