I'm almost sure it is File History's fault. I am using a second utility (Microsoft SyncToy) to manually backup my files on a different external hard drive and it didn't find any modified files when I run again the backup. This means the files where not modified. Unless** there was some minor attribute change on the files which SyncToy didn't catch, File History has a major bug!
** Just to cover this narrow possibility, I'm wondering if it could be Nero's indexing service (Nero Scout or Nero Home, I'm not sure about the name) or any other program that access user files.