Hey Matthew,
the Markdown plugin currently does not compile on GTK 2.16, more specific with GLib < 2.26. See http://nightly.geany.org/misc/build_gtk216_plugins_stderr.log for details.
One issue is that "uint" (conf.c:245) is not defined. I guess this is just a typo and should be "guint". I just don't understand why this works on other systems, like the nightly build environment for ArchLinux. Anyway, changing it to "guint" is probably good enough.
Though there is another issue: g_object_class_install_properties is first available in GLib 2.26 (used in conf.c:372). So maybe this plugin needs a higher GLib requirement.
Regards, Enrico