5
Not all text editors are created equal. Notepad in particular is terrible at interpreting line breaks that use a syntax different from Windows' default.
So just because it looks wrong doesn't mean it is wrong.
The only thing that matters is whether your server reads the files the right way or not. In some isolated cases, a server will not read the files as expected.
I would look for a server based solution, change some setting related to how it reads linkbreaks, rather than altering the files. Altering the files is treating the symptom, not the problem. The problem is with your server.
Unfortunately, I do not know anything about server configuration options that may be relevant here. Sorry.
--Julian