yea it's a little weird -- this is what i do and it works
first to do background foregrond color in emacs in a file in your home dir first
.Xdefaults
used to be
.Xresources
so now i make both

cause i can't remember which
read it in without logging out with "xrdb ~/.Xdefaults"
Code:
emacs.background: black
emacs.foreground: wheat
emacs.pointerColor: Orchid
emacs.cursorColor: Orchid
emacs.bitmapIcon: on
emacs.font: *fixed-bold-r-*-15-*-*
emacs.geometry: 107x40
ok then i put the background color i want at the very end of ~/.emacs
with
Code:
(setq initial-frame-alist
(cons
'(background-color . "#010B45")
initial-frame-alist))