Macs use CR. Linux uses LF. Windows uses CR-LF, so it would be very odd for the Windows operating system to not insert an LF after the CR. Maybe I am missing something here.
Edited on Windows -> Viewed on Linux = OK
Edited on Windows -> Viewed on Mac = OK
So I'm guessing it could be your FTP client. Make sure to upload plain text files as ASCII, not binary.
Answer
Solution:
In Notepad++, you should be able to do an EOL conversion to Windows Format, as reported in this SuperUser.com answer.