This is possibly due to a legacy startup setting in Aquamacs. You have a couple of options to fix it.
Patch Aquamacs
Try the patch posted here, which worksforme.
--- Contents/Resources/lisp/aquamacs/macosx/aquamacs-frame-setup.el.orig 2017-04-06 14:38:45.000000000 -0400
+++ Contents/Resources/lisp/aquamacs/macosx/aquamacs-frame-setup.el 2017-04-06 16:30:54.000000000 -0400
@@ -79,7 +79,7 @@
'((create-frame-min-width 68)
;; do not set any fonts here. aquamacs.el takes care of this,
;; checking that the fonts actually exist.
- (default-frame-alist
+ (initial-frame-alist
((foreground-color . "Black") (background-color . "White")
(cursor-type . box) (cursor-color . "Red")
(vertical-scroll-bars . right)
Edit your init-file
In your ~/.emacs
or ~/.emacs.d/init.el
or ~/Library/Preferences/Aquamacs Emacs/Preferences.el
(where ever you load your theme from, add (setq default-frame-alist nil)
before you load your theme, a la:
(when window-system
(when (featurep 'aquamacs)
(setq default-frame-alist nil))
(load-theme 'my-new-theme t))
Or, more simply:
(setq default-frame-alist nil)
(load-theme 'my-new-theme t)