If your source data files come from a *nix machine, chances are that they use just a single \n character as a line ending
$nix_line_ending = "\n";
One windows machines, notepad only interprets windows-style line endings as calling for a new line:
$windows_line_ending = "\r\n";
Why? convention I suppose.
You can either encourage folks to use a good text editor to read the file OR you can replace all the "\n" chars in your source files with "\r\n". Check [man]str_replace[/man].