No answer, but something like this was also posted on SO:
https://emacs.stackexchange.com/questions/37828/org-mode-doesnt-align-column-bars-properly

John

-----------------------------------
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu


On Mon, Jan 1, 2018 at 8:01 PM, Christopher Genovese <genovese@cmu.edu>
wrote:

> I make heavy use of org tables, often relying on the automatic realignment
> with C-c C-c or TAB. But after updating org-mode to 9.1.5, this realignment
> has started to lead to quite significant problems in the tables'
> appearances.
> I'm on Mac OS X 10.12.6, running Gnu Emacs 26.0.50 installed via homebrew.
> I installed org-mode 9.1.5 using the org-plus-contrib package with the
> standard
> package mechanism.
>
> I've run all these examples using emacs -Q with a minimal load of
> org-plus-contrib (configuration #1 below) as well as my own set up
> (configuration #2 below). Same results both ways.
>
> I've attached images to this email to show the results, but I'll try to
> reproduce them here as well in a fixed-width typeface.
>
> Here is a sample table as a baseline, put in a file by itself.
>
> | Date       | Time | Aerobic                     |
> Lifting                      | Strengthening          |
> Stretching             | Other | Notes |
> | 2017 01 01 | 1100 | True:34, Ladder:10, Bike:10 | Light biceps, light
> forearms | Light Shoulders, Wrist | Calf, Hamstring, Groin |       |       |
>
> With certain changes to these fields, automatic alignment of the columns
> with either C-c C-c or TAB fails horribly in several ways. The baseline
> table
> image is align-Q-baseline.png.
>
> 1. Change Time column from 1100 to any alphanumeric string *that
>    includes a letter* and the alignment works as normal.
>    (Image: align-Q-baseline.png). Note that 1100 also keeps the alignment
>    normal (align-Q-equal-number.png) but only because it is the same length
>    as Time.
>
> 2. Change Time to a short number, like 11, and the table appears as
>
> | Date       | Time | Aerobic                     |
> Lifting                      | Strengthening          |
> Stretching             | Other | Notes |
> | 2017 01 01 |     T e 4 L der:10, Bike:10 | Light biceps, light forearms
> | Light Shoulders, Wrist | Calf, Hamstring, Groin |       |       |
>
>    (Image: align-Q-short-number.png)
>
> 3. Change Time to a long number, like 111000, and the table appears as
>
> | Date       |  m | e b                      |
> Lifting                      | Strengthening          |
> Stretching             | Other | Notes |
> | 2017 01 01 | 111000 | True:34, Ladder:10, Bike:10 | Light biceps, light
> forearms | Light Shoulders, Wrist | Calf, Hamstring, Groin |       |       |
>
>    (Image: align-Q-long-number.png, similarly align-Q-confirm.png with
> 11000 instead.)
>
> 4. Change Date to include -'s (2017-01-01) and the table appears as
>
> |     Date | Time | Aerobic                     |
> Lifting                      | Strengthening          |
> Stretching             | Other | Notes |
> | 2017-01-01 | 1100 | True:34, Ladder:10, Bike:10 | Light biceps, light
> forearms | Light Shoulders, Wrist | Calf, Hamstring, Groin |       |       |
>
> Other similar problems occur as well.
>
> Again, these appear after either C-c C-c or a TAB in a field, nothing else.
> The contents are not changed only the appearance and cannot
> be fixed by editing. Killing the buffer and reopening makes the
> table look correct, but any additional realignment messes it up again.
>
> And just to be clear, this did not occur prior to installing 9.1.5,
> even a few days back. I don't recall the previous version I had
> installed. It was relatively recent but could have been a few
> steps back.
>
> Thanks, Chris
>
> --------------------------------
> Configuration #1:
>
> Emacs  : GNU Emacs 26.0.50 (build 1, x86_64-apple-darwin16.7.0, NS
> appkit-1504.83 Version 10.12.6 (Build 16G29))
>  of 2017-08-29
> Package: Org mode version 9.1.5 (9.1.5-1-gb3ddb0-elpaplus @
> /Users/genovese/.emacs.d/elpa/org-plus-contrib-20171225/)
>
> current state:
> ==============
> (setq
>  org-src-mode-hook '(org-src-babel-configure-edit-buffer
>              org-src-mode-configure-edit-buffer)
>  org-after-todo-state-change-hook '(org-clock-out-if-current)
>  org-metadown-hook '(org-babel-pop-to-session-maybe)
>  org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
>  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-eldoc-load)
>  org-archive-hook '(org-attach-archive-delete-maybe)
>  org-confirm-elisp-link-function 'yes-or-no-p
>  org-agenda-before-write-hook '(org-agenda-add-entry-text)
>  org-metaup-hook '(org-babel-load-in-session-maybe)
>  org-bibtex-headline-format-function #[257 "\300 \236A\207" [:title] 3
> "\n\n(fn ENTRY)"]
>
>
>
>
> Configuration #2:
>
> Emacs  : GNU Emacs 26.0.50 (build 1, x86_64-apple-darwin16.7.0, NS
> appkit-1504.83 Version 10.12.6 (Build 16G29))
>  of 2017-08-29
> Package: Org mode version 9.1.5 (9.1.5-1-gb3ddb0-elpaplus @
> /Users/genovese/.emacs.d/elpa/org-plus-contrib-20171225/)
>
> current state:
> ==============
> (setq
>  org-src-mode-hook '(org-src-babel-configure-edit-buffer
> org-src-mode-configure-edit-buffer)
>  org-after-todo-state-change-hook '(org-clock-out-if-current)
>  org-metadown-hook '(org-babel-pop-to-session-maybe)
>  org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
>  org-archive-location "~/org/archive::"
>  org-mode-hook '(my-org-table-extensions turn-on-font-lock my/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-eldoc-load)
>  org-archive-hook '(org-attach-archive-delete-maybe)
>  org-confirm-elisp-link-function 'yes-or-no-p
>  org-agenda-before-write-hook '(org-agenda-add-entry-text)
>  org-metaup-hook '(org-babel-load-in-session-maybe)
>  org-bibtex-headline-format-function #[257 "\300 \236A\207" [:title] 3
> "\n\n(fn ENTRY)"]
>  org-babel-pre-tangle-hook '(save-buffer)
>  org-file-apps '((auto-mode . emacs) (directory . emacs) (system . "open
> %s") ("\\.mm\\'" . default)
>                  ("\\.x?html?\\'" . system) ("\\.pdf\\'" . system)
>                  ("\\.\\(?:png\\|jpe?g\\|gif\\|tiff?\\|bmp\\)\\'" .
> system)
>                  ("\\`\\(?:.*/\\)?[^.]+\\'" . emacs))
>  org-tab-first-hook '(org-babel-hide-result-toggle-maybe
> org-babel-header-arg-expand)
>  org-babel-load-languages '((emacs-lisp . t) (R . t) (python . t) (clojure
> . t) (latex . t)
>                             (lisp . t) (haskell . t) (C . t) (ruby . t)
> (org . t) (css . t)
>                             (sass . t) (dot . t) (java . t) (ocaml . t)
> (calc . t) (ditaa . t)
>                             (sql . t) (asymptote . t))
>  org-load-hook '(my/org-load-hook)
>  org-hide-emphasis-markers t
>  org-export-backends '(ascii beamer html icalendar latex md texinfo deck)
>  org-babel-python-command "python3"
>  org-occur-hook '(org-first-headline-recenter)
>  org-ditaa-jar-path "~/bin/ditaa.jar"
>  org-structure-template-alist '(("s" "#+begin_src ?\n\n#+end_src")
>                                 ("e" "#+begin_example\n?\n#+end_example")
>                                 ("q" "#+begin_quote\n?\n#+end_quote")
>                                 ("v" "#+begin_verbatim\n?\n#+end_
> verbatim")
>                                 ("V" "#+begin_verse\n?\n#+end_verse")
>                                 ("c" "#+begin_center\n?\n#+end_center")
>                                 ("l" "#+begin_latex\n?\n#+end_latex")
> ("L" "#+LaTeX: ")
>                                 ("h" "#+begin_html\n?\n#+end_html") ("H"
> "#+HTML: ")
>                                 ("a" "#+begin_ascii\n?\n#+end_ascii")
> ("A" "#+ASCII: ")
>                                 ("i" "#+INDEX: ?") ("I" "#+INCLUDE: %file
> ?"))
>  org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
> org-cycle-show-empty-lines
>                   org-optimize-window-after-visibility-change)
>  org-todo-keywords '((sequence "TODO" "WAIT" "DONE"))
>  org-speed-command-hook '(org-speed-command-activate
> org-babel-speed-command-activate)
>  org-tags-column -116
>  org-babel-tangle-lang-exts '(("asymptote" . "asy") ("ocaml" . "ml")
> ("java" . "java")
>                               ("ruby" . "rb") ("D" . "d") ("C++" . "cpp")
> ("haskell" . "hs")
>                               ("lisp" . "lisp") ("latex" . "tex")
> ("clojure" . "clj")
>                               ("python" . "py") ("emacs-lisp" . "el")
> ("elisp" . "el"))
>  org-confirm-shell-link-function 'yes-or-no-p
>  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")
>                        ("ipynb" :follow ein:org-open :help-echo "Open
> ipython notebook." :store
>                         ein:org-store-link)
>                        ("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-tag-faces '(("urgent" . font-lock-warning-face))
>  org-todo-keyword-faces '(("WAIT" . org-wait-face))
>  org-src-window-setup 'current-window
>  )
>
>