CCleaner shouldn't be causing Chldsk to load on startup, but try these commands.
Go to Start > Type in "cmd" into Search Box. Open command prompt and run the following commands...
fsutil dirty query d: (This command should report a dirty drive)
CHKNTFS /X D: (Stops chkdsk from running at boot)
Reboot your PC
Open up Command Prompt again and run this command..
Chkdsk /f /r d:
Please be aware, you may need to run Command Prompt as Administrator. These commands worked on older versions of Windows, so I'm not sure if they do work on 7, but if they do, all the better