I have been using the todo functionality for quite a while. I also
adapted it to my needs, for instance using multiple keywords, not just
the simple cycle TODO -> DONE -> "nothing" additionally I use my
personal "coloring" and other adaptations.

When I upgraded my OS (from fedora 38 to 39) a few days ago, also emacs
was upgraded (to 29.1, before it was some 28.x version). At any rate,
the handling of the TODO-items no longer follows my choices. My settings
for instance include

(setq org-todo-keywords
      '((sequence "TODO(t)"  "UNDERWAY(w)" "DELEGATED(g)"  "PENDING(p)" "DEFERRED(l)" "|" "DONE(!)" "DORMANT(s)" "CANCELLED(c)")
        (sequence "IDEA" "CONCEPT" "UNDERWORK"  "UNDERREVISION"  "|"  "SUBMITTED" "REJECTED"  "PUBLISHED" "QUIESCENT")
        (sequence "BUG" "|"  "FIXED")
    (sequence "QUESTION" "|"  "ANSWERED")    
    ));;

(setq org-todo-keyword-faces
      '(("TODO"      . (:foreground "orange" :weight bo"~/priv/org/" ld))
    ("UNDERWAY"  . org-warning)
    ("DEFERRED"  . shadow)
    ("DELEGATED"  . (:foreground "yellow" :weight bold))
    ("PENDING"  . (:foreground "brown" shadow))
    ("DONE"  . (:foreground "green"))
    ("DORMANT"  . (:foreground "grey"))
    ("CANCELLED"  . (:foreground "grey" :weight bold))
    ))

but the cycle is the vanilla TODO->DONE->"nothing" cycle. The other
status keywords, the ones I chose as extra, are not recognised and
treated as todo-markings, and thus for instance also not specifically
colored.

I checked the documentation like

https://orgmode.org/manual/Multiple-sets-in-one-file.html

whether things have changed (I used my setting for quite a while without
crucial changes), but it seems I still follow the "syntax" of the
setting.

Any idea what's wrong, resp. whether I missed some relevant changes in
behavior?

thanks, Martin

PS: My org version is Org mode version 9.5.2 (release_9.5.2-286-gd01235)