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-default-notes-file "~/.emacs.d/xxxxxxx.org"
 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-agenda-files '("~/org/xxxxxx/xxxxxx.org" "~/org/xxxxxx/xxxxxxx.org"
"x:/xxxxxx/xxxxxx.org" "x:/xxxxxxx/xxxxxxx.org")
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 )
-- 
Mit freundlichen Grüssen / With kind regards:
Jens Lange