By default, eBookBinder uses the Perl version of MultiMarkdown 2. If you want to use the newer version of MultiMarkdown, you must first install the appropriate MultiMarkdown Terminal tool, as there are no new Perl versions of MultiMarkdown since MultiMarkdown version 3.
Setting up the MultiMarkdown Terminal Tool for eBookBinder is a straightforward process eBookBinder Preferences under the tab MultiMarkdown by following the step-by-step installation.