One issue is that Windows tends to use "\r\n" (carriage-return line-feed) at the end of each line, while Linus (and other *nixes) use simply "\n". I think Notepad++ should have a setting to save in the appropriate format, somewhere in the preferences (I know that Notepad2 does).
If you open the files in vi, you are likely to see that they have "^M" at the end of each line. Entering the following command should solve the problem:
Code:
:1,$ s/<Ctrl-V><Ctrl-M>//
By Ctrl-V I mean (of course) "hold down the Ctrl key and press V" (likewise with M) - This will enter a "^M" character. 1,$ addresses every line from first to last.
Hope this helps.
Rob