There have been a good number of bug fixes made to MultiMarkdown, and a lot of updates to the documentation. I am waiting for the results of some testing to come back before I release the next update.
Most significantly, MMD has been updated to the Markdown 1.02b8 codebase (released last week), the Mac drag-and-drop apps have been completely rewritten, and a complete overhaul of XML namespaces has occurred. There have been some improvements made to the XSLT files as well, and I have released an update engine file for TeXShop.
I hope to hear back from some testers in the next day or two, and if not will release without their input.
Thank you for your patience!