I encountered these issues this morning when I updated Org from trunk (and reloaded it with C-c C-x !). I believe it's following commit "Split `org-emph-re' and `org-verbatim-re'". I've got 2 issues:
1. Nothing longer than one character has emphasis. I find changing the 4th element of org-emphasis-regexp-components ("body-regexp") to ".*?" fixes this. 2. Headings of level >= 3 are fontified as if they were emphasized. I'm guessing org-do-emphasis-face is considering "***" as an acceptable emphasis string. If it helps, this is my setting for org-emphasis-regexp-components: (defconst org-emphasis-regexp-components '(" \t('\"{<“‘–" "- \t.,:!?;'\")}\\[>”’–…" " \t\r\n" ".*?" 0)) -- Ian Dunn