I assume that you are remotely automating an ftp transfer. And my guess is that you did not enable binary mode for the transfer, and/or did not use binmode on the local filehandle when writing to the file. But unless you show code, we won't be able to tell.

Did you do a sanity check and compare what size Perl reports via -s against what the operating system reports (via dir, or via the property sheet in Explorer) ?