What exactly is the problem? If you want to know why $/ is messing with you, a quick trip to the perldoc provides the answer:

The output record separator for the print operator. Ordinarily the print operator simply prints out its arguments as is, with no trailing newline or other end-of-record string added. To get behavior more like awk, set this variable as you would set awk's ORS variable to specify what is printed at the end of the print. (Mnemonic: you set "$\" instead of adding "\n" at the end of the print. Also, it's just like $/, but it's what you get "back" from Perl.)

Which means that when Archive::Zip calls 'print' to output a chunk of it's generated binary data, perl appends a '\n' to the end of every chunk. Thus corrupting the archive.