Have you checked to make sure the file format is what perl as compiled expects? Did you look at the file with a hex editor to make sure the EOLs are as they are supposed to be?

The null could be because you have what it thinks are two end of lines back to back. They might not display correctly in windows (if it is expecting a *nix type EOL, and cygwin perl can expect that.)

In the code section, it would not cause problems since blank lines are okay. I know it is not supposed to work like that, but I have had that issue exactly bite me in the past, and there is no way any of us would see it as things are posted to the web page.

The fact that it works with the line
#    next if not $line;
uncommented makes me even more suspicious.

The last line of your submission, that it works fine on MacOS makes me wonder... Did you create the file on something other than windows? Or use a text editor for somethign other than windows? Happy hunting.

Good Luck.