I think the difference is probably something to do with the editor you use to edit files, and specifically the line ending characters.
DOS machines (like Windows) use a carriage return character and a line feed (“\r\n”) as a line ending, and Unix-based machines (newer Macs and Linux included) use just a single line feed character (“\n”). When files are transferred back and forth between the two different systems and through different text editors, those line breaks get converted in different ways.
I wouldn’t worry about it, unless it really seriously bugs you. Most text editors can be configured to recognize different EOL characters and account for them or convert them to your desired format. And if not, there’s always find/replace.