It sounds as if you're on a Windoze system, and your host is using UNIX, and you aren't uploading in ASCII mode.

In text files (including Perl source), Windows uses a carriage return and a line break at the end of every line, Macs use a carriage return only, and UNIX uses a line break only.

To counteract that, upload all non-image files in ASCII mode, and all images in binary mode in your FTP client.