Previously, C-x C-s in an org-edit-special buffer (invoked via C-') would save the underlying org buffer (provided (setq org-src-window-setup (quote current-window)) was set; it was buggy with other settings, see http://thread.gmane.org/gmane.emacs.orgmode/50979 for discussion). Currently, C-x C-s prompts to save the temporary source edit buffer in a new file, which is almost certainly not what the user intends. I hope someone can look into this, C-x C-s shouldn't be broken in any context.
This broke some time between commit fc93b6f34071703d5a154a51540f3f4e3f15b8a2 (Jan. 18) and this week, _possibly_ as a result of the change ensuring that buffer-file-name is nil in temporary org-src buffers. Buffer-file-name not being nil in a temp buffer is incorrect behavior, but in this context having C-x C-s not working is a much worse behavior, so perhaps that change ought to be reverted if it's the culprit. --Leo