Unix, Windows and MacOS use different character sequences for newlines. In "Binary mode", the FTP program will transfer the file as it is -- just what you expect --, whereas in "Ascii mode", it will change the newlines to those of the target system. Unfortunately, this can break binary files (like images) and generally introduces a lot of trouble. Fortunately, Perl usually doesn't have a problem with different newline sequences.

I recommend editing everything in unix newline mode (perl scripts/modules, HTML files, ...) and upload in "Binary mode" only.