I noticed some of my music files were modified (Windows 7, NTFS) when I wasn't home. They have different MD5 checksums. I looked in the Event View to see if I could find anything about what might do it. The antivirus programs don't check that drive. I manually scanned the file with the antivirus program and it says it is not infected.
Is there anyway that you have it so the program/process name which causes the "date modified" date to change?