I think the confusion is that both the Markdown (MD) and MultiMarkdown
(MMD) bundles have a convert to PDF command. The MD bundle uses
HTMLDOC to do the conversion whilst MMD uses LaTeX. I am not sure
exactly what the commands are called in the respective bundles as I
have changed both to suit my preferences. I would suggest that if you
want to use any of the MMD functionality that you delete the MMD
commands (and language) in the MD bundle and install the MMD bundle.