Not with Notepad. It happens because Notepad only understands Windows type control characters for new line and the document you try to view doesn't use that. Most other editors understand *nix and Mac returns too.
IIRC Windows uses CR LF, Unix uses CR and Mac uses LF
Funny thing I've notices is that newer versions of Notepad can read nix files locally but when I view source I still get the boxes. Beats me!