CHKDSK will run before loading Windows, and you may see a bunch of geeky stuff on the screen while it's scanning your disk. Would you like to schedule this volume to be checked the next time the system restarts?' This happens because CHKDSK cannot operate on the drive from which you have started Windows. You'll see a message informing you that 'CHKDSK cannot run because the volume is in the use by another process.
The /R option tells CHKDSK to scan for bad disk sectors, and the /F option means to fix any errors found. When the Command Prompt window appears, type CHKDSK C: /F /R then press Enter. Right-click on the CMD.EXE icon at the top of the search results, then click 'Run as administrator.' If you get a User Account Control popup, click YES to continue. To do so, click the Start button, then type CMD, but don't press Enter. On Windows, you can check your hard drive for errors (and sometimes fix them) by running the CHKDSK utility. In fact, even if you don't suspect a problem with your hard drive, it's wise to make regular backups so you can survive a hard drive failure with only minimal inconvenience. So my immediate advice is 'BACKUP YOUR HARD DRIVE!' as soon as possible. It could be a hint of horrific hardware happenings, or the drumbeat of developing data disaster. Generally a clicking sound coming from your hard drive is a Very Bad Thing.