I'm not sure why this happens. Did you shutdown your PC abruptly (holding power button, power switch etc.) while the HDD light was on? If so, you might have corrupted some files.
Here is a command that might help you:
Open Command Prompt and type (without the quotes) "chkdsk C: /f". Then, after confirming the check on next startup, restart your PC. Wait for the check to finish. Also, if there are any "deleting/fixing corrupt file/removing orphaned inode" messages, please take note of them and post them.
Hope this helps,
Bajiru