legacy MS Windows has several ways of hiding files from you, some better known than others.

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I'd very strongly suggest you boot the system with another OS, inventory the drive, and run MD5 checksums on all executables. Particularly, note the ones that change. Debian's going to bypass virtually all of NTFS's security. Being able to compare images at different times would also be useful.

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A friend recommends [link|http://www.sysinternals.com/|sysinternals.com] as a useful site for forensics tools.

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