Solved. For anyone else who has this problem, this is what worked for me. I uninstalled all versions of multimarkdown on my computer, then uninstalled scrivener beta, then installed a fresh copy of scrivener beta.
It looks like we might have been using some obsolete command-line flags (the embedded version was quite old, as you might have noticed). The next beta will have the latest version of MMD and be fixed to run it correctly—so in theory you should be able to install it separately as well again.