emacs - Aquamacs overrides my custom-set-faces options

I've just installed Aquamacs on my Mac.

I have a .emacs file in my home, which contains all my customizations. Among these, I have:

(custom-set-faces
 '(default ((t (:stipple nil :background "black" :foreground "grey70" :inverse-video nil :box nil :strike-through nil :overline nil :underline nil :slant normal :weight normal :height 140 :width normal :foundry "apple" :family "Monaco"))))
 '(font-lock-builtin-face ((t (:foreground "grey50"))))
 '(font-lock-comment-face ((t (:foreground "darkgreen"))))
 '(font-lock-constant-face ((t (:foreground "grey50"))))
 '(font-lock-doc-face ((t (:foreground "grey50"))))
 '(font-lock-doc-string-face ((t (:foreground "yellow2"))))
 '(font-lock-function-name-face ((t (:foreground "SteelBlue"))))
 '(font-lock-keyword-face ((t (:foreground "red"))))
 '(font-lock-preprocessor-face ((t (:foreground "SteelBlue"))))
 '(font-lock-reference-face ((t (:foreground "LightSkyBlue"))))
 '(font-lock-string-face ((t (:foreground "yellow2"))))
 '(font-lock-type-face ((t (:foreground "violet"))))
 '(font-lock-variable-name-face ((t (:foreground "orange"))))
 '(font-lock-warning-face ((t (:foreground "grey50"))))
 '(isearch ((t (:background "yellow4" :foreground "black"))))
 '(mode-line ((t (:background "grey90" :foreground "black"))))
 '(text-mode-default ((t nil)))
 '(zmacs-region ((t (:background "grey70" :foreground "black")))))

This block seems not to be applied automatically.

If I select the lines from the .emacs and manually evaluate them, everything works fine. My guess is that these options are overridden in some other place.

How can I debug this? Where should I set my custom faces?

UPDATE:

According to this, preferences should be loaded in the following order:

 ~/.emacs  (deprecated -- meaning 'should not be used
 for new installations, but will continue to be supported' -- in Aquamacs on OS X)
 customizations saved by request or automatically by Aquamacs in customizations.el
 /Library/Preferences/Emacs/Preferences.el
 /Library/Preferences/Aquamacs Emacs/Preferences.el
 ~/Library/Preferences/Emacs/Preferences.el
 ~/Library/Preferences/Aquamacs Emacs/Preferences.el

My ~/Library/Preferences/Aquamacs Emacs/Preferences.el looks like (by default):

 (load "~/.emacs")

So this doesn't really make sense to me...