Emacs first boot won't install all packages from package-selected-packages

Question

I've got this in my init.el:

(require 'package)
(package-initialize)
(setq package-enable-at-startup nil)

(setq package-archives '(("ELPA"  . "http://tromey.com/elpa/")
             ("gnu"   . "http://elpa.gnu.org/packages/")
             ("melpa" . "https://melpa.org/packages/")
             ("org"   . "https://orgmode.org/elpa/")))

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;;; Bootstrapping use-package
(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))

(eval-when-compile (require 'use-package))

(use-package use-package
  :config
  (setq use-package-always-ensure t))

As far as I understand, this should be good to install all the packaged listed in

'(package-selected-packages
   (quote
    (org org-plus-contrib org-ref techela tuareg haskell-mode gnuplot gnuplot-mode helm-ispell ac-ispell paredit ox-tufte auctex json org-grep iedit wgrep helm geiser slime-company company-jedi zzz-to-char rainbow-delimiters avy ivy projectile twittering-mode zerodark-theme pretty-mode flycheck-clang-analyzer flycheck-irony flycheck yasnippet company-c-headers company-shell company-irony irony irony-mode company-lua mark-multiple expand-region popup-kill-ring dmenu ido-vertical-mode ido-vertical ox-html5slide centered-window-mode htmlize ox-twbs diminish erc-hl-nicks symon rainbow-mode switch-window dashboard smex company sudo-edit emms magit org-bullets hungry-delete beacon linum-relative spaceline fancy-battery exwm use-package)))

which is inside my custom-set-variables. However, when I do a first-time, clean (no existing elpa/ directory) startup of Emacs reading this init.el, not all of the packages are gotten and installed. But then I can do a package-install-selected-packages and, Emacs reports that it doesn't have anything in package-selected-packages. Looking at the variable confirms this. What could be going wrong? An older "working" version of this (with existing elpa/ directory) responds oddly to package-install-selected-packages, wanting to install e.g., auctex and some nine other packages that the package code above apparently isn't seeing or dealing with. I'm baffled as to why package-selected-packages seems to be so flaky for me. I'm assuming my older .emacs.d with the existing elpa/ has install info that is "working around" this failing package-selected-packages situation.