I'd recommend never to edit files intended for Unix systems on Notepad. Not only are the line terminators a problem, the UTF-8 encoding can also be a problem. Notepad seems to append BOM to the beginning of files with UTF-8 encoding, which usually causes problems.

So, if you want to use scripts on N9 preferably wrtie them directly on N9 using nano or some other editor. Or if you want to do it in Windows, use some editor that can write with LF line terminators instead of CR/LF. Crimson Editor comes to mind off the top of my minfd.