Restarting emacs changes default font

I'm new to Emacs. Been a vim user.

Using M-x customize-face, irrespective of what font I set it to, Emacs always ends up using Inconsolata-g for Powerline font. Default is DejaVu Sans Mono. I tried removing .emacs.d directory as well as emacs (package itself), but neither helps.

Here's what I do:

1. M-x customize-face default
2. Set it to, say, Ubuntu Mono Regular
3. Hit Apply and things look good
4. So I hit State and choose option #1 which stores it to ~/.emacs (for fresh install; I use ~/.emacs/init.el instead - not sure which is better of two)
5. C-x C-c
6. Start emacs again and the font is set back to Inconsolata-g for Powerline

How do I get rid of what I'm seeing on step 6 here? I saved ~/.emacs to ~/.emacs.d/init.el and here are its contents:

$ cat .emacs.d/init.el 
(custom-set-variables
 ;; custom-set-variables 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.
 )
(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.
 '(default ((t (:inherit nil :stipple nil :inverse-video nil :box nil :strike-through nil :overline nil :underline nil :slant normal :weight normal :height 130 :width normal :foundry "PfEd" :family "Ubuntu Mono Regular")))))