Because the file got slightly changed either when being written to the flash drive, or while being read from the flash drive.
Unix and Windows bump heads when it comes to text files because of the way that each OS handles new lines. This is only supposed to apply to text files, but if a map is being interpreted as a text file when it's really a binary file and the conversion is still being done somewhere then it would essentially corrupt the map. I just copied my entire map folder from Linux->Windows no problems, and I've done the other direction a few times without problems. I've never tried it with a flash drive, though.