org-agenda-mode relies on setting
text-properties for the faces that are used in the
*Org Agenda* buffer. When
org-agenda-mode is enabled in the
*Org Agenda* buffer, the following snippet is used to prevent
font-lock-mode from being enabled:
;; Keep global-font-lock-mode from turning on font-lock-mode
(org-set-local 'font-lock-global-modes (list 'not major-mode))
Emacs does not do well when a marriage is attempted between
text-properties to colorize text within a buffer. It is possible to some degree (with a lot of work), but probably is not recommended (nor worth the effort, in the opinion of this author). Thus, it is usually best to choose one or the other.
In this particular case, the original poster indicated that
font-lock-mode was enabled by using
rainbow-mode thus resolved the issue.
Overlays play well with both
text-properties. So perhaps the original poster could find a minor-mode that does not use
font-lock to achieve the desired visual effect.
It is possible to create a custom
org-agenda-mode that uses
font-lock instead of
text-properties [which is what this particular author has done], but that entails a lot of work and is ultimately a custom setup tailored to the needs of an individual user.