Greetings,
I doubt that this is a bug in Net::FTP, though stranger things have happened. I would suggest taking a look at this neat little script from CPAN.

Here is its description:

With this script you can check if a text file is of
a specific type and convert it to a different type.
Special feature is the ability of fixing files that were
broken by wrong ftp upload and download mode (ascii/bin).
Supported file types are dos, mac, unix and broken.
It also runs under DOS.
[download]

This may get you started in the right direction and is obviously not a permanent solution.

Hope this helps, cheers, and happy hacking - L~R