I can think of a few possibilities, but they are not all-inclusive:
- The files may be in a form where they must occupy contiguous disk memory. Defragmenting the USB drive may fix this.
- The file may contain a code combination which is an escape sequence for USB.
- The format (as opposed to the file) of the hard disk may have tangled links. Do a chkdsk (or equivalent) on the source disk.
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