I agree with a reinstall being the best method. Sometimes viruses or spyware programs download and install all sorts of hidden junk on your computer.
Better than reinstalling, though, would be to make a backup image of your hard drive after you have everything reinstalled and updated. Then if anything happens that requires a reinstall all you need to do is restore your hard drive from the backup image, which saves a great deal of time. Basically the same as reinstalling but a lot more convenient.
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