What exactly did you do?
===================
1. Configure block below in custom-set-variables.
'(org-emphasis-alist
(quote
(
("!" org-habit-overdue-face)
("%" org-habit-alert-face)
("*" bold)
("/" italic)
("_" underline)
("=" org-verbatim verbatim)
("~" org-code verbatim)
("+" (:strike-through t))
)))
2. Type %blabla% and !blabla! in org-mode
What did you expect to happen?
=========================
%blabla% should show in in yellow and without %
!blabla! should show in red and without !
What happened instead?
===================
%blabla% is shown normal
!blabla! is shown normal
What's more?
===========
I think it broke with the 9.1 release.
Emacs : GNU Emacs 25.2.1 (x86_64-w64-mingw32)
of 2017-04-24
Package: Org mode version 9.1.1 (9.1.1-1-g80cbf9-elpa @ x:/folder/user/.emacs.d/elpa/org-20170918/)
current state:
==============
(setq
org-tab-first-hook '(org-babel-hide-result-toggle-maybe org-babel-header-arg-expand)
org-agenda-clockreport-parameter-plist '(:lang "de" :maxlevel 6 :fileskip0 t :properties ("XXXXXXXX" "XXXXXXXX" "XXXXXXXX") :indent t :narrow 80!)
org-speed-command-hook '(org-speed-command-activate org-babel-speed-command-activate)
org-download-screenshot-method "convert clipboard: %s"
org-ellipsis "↴"
org-occur-hook '(org-first-headline-recenter)
org-src-tab-acts-natively t
org-metaup-hook '(org-babel-load-in-session-maybe)
org-clock-into-drawer nil
org-protocol-protocol-alist '(("outlook" :protocol "outlook" :function org-protocol-outlook :kill-client t))
org-confirm-shell-link-function 'yes-or-no-p
org-finalize-agenda-hook '(org-agenda-to-appt)
org-highlight-latex-and-related '(latex script entities)
org-emphasis-alist '(("!" org-habit-overdue-face) ("%" org-habit-alert-face) ("*" bold) ("/" italic) ("_" underline) ("=" org-verbatim verbatim) ("~" org-code verbatim)
("+" (:strike-through t)))
org-return-follows-link t
org-todo-keyword-faces '(("ZU-ERLEDIGEN" . "white") ("IN-ARBEIT" . "red") ("UNTERBROCHEN" . "orange") ("WARTEN-RÜCKM-KUNDE" . "yellow")
("WARTEN-RÜCKM-INTERN" . "yellow") ("WARTEN-WARE" . "yellow") ("ERLEDIGT" . "green") ("STORNIERT" . "green"))
org-agenda-include-diary t
org-startup-indented t
org-after-todo-state-change-hook '(org-clock-out-if-current org-protocol-delete-msgs-on-task-done)
org-from-is-user-regexp nil
org-src-mode-hook '(org-src-babel-configure-edit-buffer org-src-mode-configure-edit-buffer)
org-tags-column -1
org-agenda-before-write-hook '(org-agenda-add-entry-text)
org-babel-pre-tangle-hook '(save-buffer)
org-mode-hook '(#[0 "\300\301\302\303\304$\207" [add-hook change-major-mode-hook org-show-block-all append local] 5]
#[0 "\300\301\302\303\304$\207" [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-bibtex-headline-format-function #[257 "\300 \236A\207" [:title] 3 "\n\n(fn ENTRY)"]
org-archive-hook '(org-attach-archive-delete-maybe)
org-agenda-time-grid nil
org-yank-adjusted-subtrees t
org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers org-cycle-show-empty-lines org-optimize-window-after-visibility-change)
org-agenda-hide-tags-regexp ".*"
org-agenda-start-with-log-mode t
org-agenda-start-with-clockreport-mode t
org-ditaa-eps-jar-path "x:/xxxxxx/xxxxxx/.emacs.d/elpa/contrib/scripts/DitaaEps.jar"
org-use-property-inheritance t
org-download-annotate-function 'org-download-annotate-default
org-todo-keywords '((sequence "ZU-ERLEDIGEN" "IN-ARBEIT" "UNTERBROCHEN" "|" "ERLEDIGT" "STORNIERT")
(sequence "WARTEN-RÜCKM-XXXXX" "WARTEN-RÜCKM-XXXXX" "WARTEN-XXXXX" "|"))
org-hide-emphasis-markers t
org-clock-report-include-clocking-task t
org-download-image-dir "~/temp"
org-agenda-span 'day
org-catch-invisible-edits 'error
org-babel-tangle-lang-exts '(("latex" . "tex") ("emacs-lisp" . "el") ("elisp" . "el"))
org-confirm-elisp-link-function 'yes-or-no-p
org-metadown-hook '(org-babel-pop-to-session-maybe)
org-ditaa-jar-path "x:/xxxx/xxxxxx/ditaa0_9.jar"
org-startup-truncated nil
org-link-parameters '(("id" :follow org-id-open) ("rmail" :follow org-rmail-open :store org-rmail-store-link) ("mhe" :follow org-mhe-open :store org-mhe-store-link)
("irc" :follow org-irc-visit :store org-irc-store-link) ("info" :follow org-info-open :export org-info-export :store org-info-store-link)
("gnus" :follow org-gnus-open :store org-gnus-store-link)
("docview" :follow org-docview-open :export org-docview-export :store org-docview-store-link)
("bibtex" :follow org-bibtex-open :store org-bibtex-store-link)
("bbdb" :follow org-bbdb-open :export org-bbdb-export :complete org-bbdb-complete-link :store org-bbdb-store-link)
("w3m" :store org-w3m-store-link) ("file+sys") ("file+emacs") ("outlook" :follow org-outlook-open :export nil) ("doi" :follow org--open-doi-link)
("elisp" :follow org--open-elisp-link) ("file" :complete org-file-complete-link) ("ftp" :follow (lambda (path) (browse-url (concat "ftp:" path))))
("help" :follow org--open-help-link) ("http" :follow (lambda (path) (browse-url (concat "http:" path))))
("https" :follow (lambda (path) (browse-url (concat "https:" path)))) ("mailto" :follow (lambda (path) (browse-url (concat "mailto:" path))))
("news" :follow (lambda (path) (browse-url (concat "news:" path)))) ("shell" :follow org--open-shell-link))
org-babel-load-languages '((ditaa . t) (latex . t))
org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
)