There is a bug in Windows where the last modification date & times of .eml files are changed. To fix this you must delete the following registry key:
Note that to do this you should run regedit.exe as Administrator. You may also need to change the keys permissions to delete it (right click on the .eml key entry and choose Permissions, then Advanced, set the owner to the current user or Administrators, then check the Allow box for Full Control for the permissions of Administrator and click OK).
Also be aware that if you re-install Windows Live Mail then it will recreate this registry key and so the problem will occur again. If you do re-install Windows Live Mail then you must delete the registry key again.