The .DS_Store files should be created on any type of volume or share (SMB or AFP, etc) so I don't think that's it. I wonder if it's getting some file system extended attribute added, though this should not change the actual hash of the file itself. Could you ssh in and inspect a bait file before mounting it on your Mac? Try running xattr /path/to/file and see what it returns and then run it again after mounting the share on your Mac.