Why does check disk run on every startup?

Nice October 14, 2012
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Every time I turn on my laptop, the check disk continues to run until I cancel it. This is happening only from couple of days since I ended up deleting some file from my C drive by mistake. After logging in I get an alert that $mft is missing. I think the file that I did shift+del on is related to scan disk.

Has anyone faced this error or has a solution for this? Any help will be greatly appreciated!

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