These are from two differently colored TODO cookies, not DONE
cookies.
There are text properties here:
face (:inherit hl-todo :foreground "#cc9393")
fontified t
org-category "research"
org-stats 0
There are text properties here:
face org-todo
fontified t
org-category "research"
org-stats 0
I don't use the hl-todo package. But looks like you do, and it somehow highlights only some "TODO" keywords based on some regexp.
How about disabling hl-todo completely in Org files, and then see if you still get that difference in faces?