On clock-out in the .notes buffer, tasks in the buffer get removed. Steps to produce this behaviour: 1. start emacs with --no-init 2. M-x org-capture 3. t ( for task ) 4. type "A1" for the subject, then type C-c C-c The task will get added to the .notes buffer. Then from the .notes buffer do this: 5. M-x org-capture 6. t ( for task ) 7. type "B1" for the subject, then type C-c C-c then 8. clock-in to the "A1" task (C-c C-x C-i), then 9. clock-out (C-c C-x C-o) the B1 task will get removed from the buffer on step 9. Emacs : GNU Emacs 24.3.50.1 (x86_64-pc-linux-gnu) of 2013-12-15 on gkar, modified by Debian Package: Org-mode version 8.2.3a (release_8.2.3a @ /usr/share/emacs/24.3.50/lisp/org/) current state: ============== (setq org-tab-first-hook '(org-hide-block-toggle-maybe org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe org-babel-header-arg-expand) org-speed-command-hook '(org-speed-command-default-hook org-babel-speed-command-hook) org-occur-hook '(org-first-headline-recenter) org-metaup-hook '(org-babel-load-in-session-maybe) org-confirm-shell-link-function 'yes-or-no-p org-after-todo-state-change-hook '(org-clock-out-if-current) org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer) org-agenda-before-write-hook '(org-agenda-add-entry-text) org-babel-pre-tangle-hook '(save-buffer) org-mode-hook '(#[nil "\300\301\302\303\304$\207" [org-add-hook change-major-mode-hook org-show-block-all append local] 5] #[nil "\300\301\302\303\304$\207" [org-add-hook change-major-mode-hook org-babel-show-result-all append local] 5] org-babel-result-hide-spec org-babel-hide-all-hashes) org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point org-babel-execute-safely-maybe) org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-hide-inline-tasks org-cycle-show-empty-lines org-optimize-window-after-visibility-change) org-confirm-elisp-link-function 'yes-or-no-p org-metadown-hook '(org-babel-pop-to-session-maybe) org-clock-out-hook '(org-clock-remove-empty-clock-drawer) )