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.