I disagree. If emacs were saving in DOS mode (which means the newlines are comprised of a ^M^J (\r\n) instead of the Unix ^J (\n)), copying the file with 'cp' should have no effect whatsoever. 'cp' does not do any conversions, so it makes 0 sense that the problem would clear up simply by coping the file to a new name. This is why I think it's a filesystem/OS issue.