With Emacs master:
   commit d213cf0400ee5cad2e7f4626745fd97b942ff5e9   Date:   Thu Jun 18 19:15:05 2015 -0400
but not Emacs 24.5, I see Emacs wipe out my custom-set-variables when I start Emacs, as it sets package-selected-packages for the first time:
diff --git a/emacs/init.el b/emacs/init.elindex 480d711..278cb80 100644--- a/emacs/init.el+++ b/emacs/init.el@@ -245,63 +245,15 @@  ;; 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.- '(Buffer-menu-name-width 64)- '(ac-delay 1.0)- '(cc-search-directories+ '(package-selected-packages    (quote-    ("." "/usr/include" "/usr/local/include/*" "./src" "../src" "./include" "../include" "./inc" "../inc" "./public" "../public" "./internal" "../internal")))- '(column-number-mode t)- '(delete-by-moving-to-trash t)- '(dired-auto-revert-buffer t)- '(ediff-merge-split-window-function (quote split-window-vertically))- '(evil-ex-hl-update-delay 0.01)- '(evil-ex-visual-char-range t)- '(evil-highlight-closing-paren-at-point-states nil)- '(evil-intercept-maps nil)- '(evil-kbd-macro-suppress-motion-error t)- '(evil-mouse-word (quote evil-move-WORD))- '(evil-move-cursor-back nil)- '(evil-overriding-maps nil)- '(evil-search-module (quote evil-search))- '(evil-shift-width my-offset)- '(ff-always-try-to-create nil)- '(ff-special-constructs nil)- '(font-lock-maximum-decoration (quote ((c++-mode . 2))))- '(frame-background-mode 'dark)- '(global-whitespace-mode t)- '(inhibit-startup-screen t)- '(inverse-video t)- '(jde-global-classpath my-java-classpath)- '(jde-jdk-registry-   (quote-    (("1.6.0" . "/usr/lib/jvm/java-1.6.0-openjdk.x86_64"))))- '(jde-sourcepath my-java-sourcepath)- '(large-file-warning-threshold 1000000000.0)- '(message-log-max 100000)- '(nxml-child-indent my-offset)- '(nxml-sexp-element-flag t)- '(python-indent my-offset)- '(python-indent-offset my-offset)- '(scroll-conservatively 101)- '(scroll-margin 4)- '(sentence-end-double-space nil)- '(show-paren-mode t)- '(tags-case-fold-search nil)- '(tool-bar-mode nil)- '(undo-tree-visualizer-diff nil)- '(undo-tree-visualizer-timestamps t)- '(whitespace-style (quote (face tabs trailing)))- '(x-select-enable-clipboard t)- '(x-select-enable-primary t))+    (goto-chg haskell-mode flylisp evil-numbers diff-hl adjust-parens)))) (custom-set-faces
*Messages* buffer shows:
Saving file /Users/boreilly/unihome/emacs/init.el...Wrote /Users/boreilly/unihome/emacs/init.el [2 times]Saving file /Users/boreilly/unihome/emacs/init.el...Wrote /Users/boreilly/unihome/emacs/init.el [2 times]
(NB: I symlink this init.el to .emacs)
These messages don't appear when starting Emacs 24.5.
Also note, my init.el calls package-initialize and package-install directly. The writes to init.el occur during a call to (package-install 'goto-chg), which is not installed.