My windows repair program didnt do this to your system. The chkdsk is part of the Windows OS, none of my stuff in my program had even ran yet
So it was Windows checking the drive and fixing any problems it found (Again this is a built in tool in Windows), the fact that it took as long as it did means that check disk found bad sectors on your drive and tried to recover the files, but if it was stopped during that then any file it was trying to recover is most likly corrupt. But most of the time it isnt able to get the data from the bad sector anyways.
Bad sectors means bad hard drive.
You need to backup your important files as soon as you can to another drive or external drive. Then once you have your data backed up and safe (Not to the same drive!) we can dig in more to confirm the drive is bad or not
Shane