I suspect it's probably filesystem overhead. There's a couple sources of it:
- HFS uses a catalog file to outline where everything is. This file is hidden, but it does take up space. Existing drives will have slightly more fragmented catalog files that could use up more space. I don't know how you are measuring the space used, so this may or may not be getting measured.
- Drives that have been in use longer will be more likely to have file fragmentation. This fragmentation does introduce a little overhead since each fragment has a header on disk. The more fragmentation, the higher this overhead becomes. Copying the files to a clean drive will produce much less fragmentation.
EDIT: One other source of difference is the block size of the drive. Since files are allocated in blocks, you get a bit of overhead from that as well due to unused parts of the blocks (bytes in the file vs bytes on disk). If the block size is smaller on this new drive, because it is a smaller drive perhaps, then it will produce a difference.