I altered, via customize, the foreground colors of muse-emphasis-2 and muse-emphasis-3. These changes appear in my .emacs as:

(custom-set-faces
;; custom-set-faces was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
'(muse-emphasis-2 ((t (:foreground "BlueViolet" :weight bold))))
'(muse-emphasis-3 ((t (:foreground "IndianRed" :slant italic :weight bold)))))

When I quit, and restarted emacs, these lines were in my .emacs, but the change in fg color did not show up either as highlighting in muse buffers, or in in the customize buffer itself.

I had to open my .emacs, and C-X C-E on the custom-set-faces expression, and then both behaved as expected (i.e., highlighting appeared, and the fg color was filled out in customize).

I'm using emacs 22.0.90.1 on Mac OSX, with the developer muse of about 2 days ago.