I would also make sure that what ever you back your files up onto is formatted using FAT16 or FAT32 and not NTFS. Don't ask why because I don't have a clue for a technical reason just have had issues with "where they hell has it got that from again" which stripping it of all its NTFS extras has solved.
There is a 'secondary data channel' on NTFS...shhhhttttt.. I dont remember what it was, I used to play with it, but you could add all kinds of additional metadata (virus stuff) and it would be there, unseen, ready to be picked up...
damn...
edit..
Alternate Data Streams..thats what it is!