One of the commits between ffdc508429c58716272743c0e0650bb721fd906a (good) and 67275f4664ce00b5263c75398d78816e7dc2ffa6 (bad) a change was introduced that broke folding for markdown blocks. I'm not sure of the exact commit because folding is completely broken for all the commits in between.
Looking at the diff between the two there are so many changes involving the invisible text property that I have no idea which one is the culprit. The markdown blocks remain visible and have the invisible text property set to nil, when folded #+end_src will turn into ... but the markdown remains visible. The whole block will be left open if any of the markdown list or heading chars are present in the block. Here are some examples that trigger the issue: * a #+begin_src markdown 1. #+end_src * b #+begin_src markdown - #+end_src * c #+begin_src markdown # hello #+end_src