Ah, looks like I figured it out. The Makefile is a bit overzealous and was killing my VirtualBox process (I'd named the docker-machine a string that started with matterm), so I added a grep exclusion to the line so that the virtualbox process didn't get killed.
In case anyone else needs it, the new line is:
@for PID in $$(ps -ef | grep [m]atterm | grep -v VirtualBox | awk '{ print $$2 }'); do \
(I added | grep -v VirtualBox)