On two systems in my office the CHKDSK did run one morning and it reported the deletion of several files. Twice in a row it did it on my system and reported deleting the same files.
I did some virus/spyware checking and found some spyware on my system. I believe it might have come from some drive recovery software my coworker with the other CHKDSK-ing system found.
Her system actually became unbootable and she had to re-install the operating system.