My bad. temp.zip/data.zip same thing. The row in the database is not changing, both systems are selecting the same data. But you made a good suggestion. If I say:

print length($inbound{'data'});
[download]

Both systems have an identical byte size. So infact it's not DBD::Mysql at all. It's happening when I write the data to the file. What would cause perl to write out extra binary data?