A Perl program that is created on Windows will have Windows line end characters (i.e. CR/LR or \015\012).
Although, just for informational purposes, it's important to note that you don't have to create files with the \r\n ending. I've been creating all of my files with \n endings for years on Windows, and it's saved me a lot of grief, particularly when ftp-ing files without worrying about setting text mode. The text editors that I've been using are jedit and vim; I'm sure there are others that can do this.