In perl-markdown, a couple of whitespaces at the end of a line are rendered as a <br /> tag. It does not appear that cl-markdown has implemented this feature yet. For example, consider the following input text (note that there are two whitespaces at the end of "First line"):

First line Second line

Output from perl-markdown: ==========================

<p>First line<br /> Second line</p>

Output from cl-markdown: ========================

<p>First line Second line</p>

Best wishes, Hans