init.el is missing many settings after emacs start

[The Grue]

Hello,

since some months, every now and then when I start emacs23, my init.el is 
missing many configuration lines. I have checked it in to a git repository, so 
I can restore the settings, but I really don't like it ;)

The diff looks like this, with many lines deleted (by me, don't want to post 
>200 lines):


diff --git a/init.el b/init.el
index 745be22..c5e83dd 100755
--- a/init.el
+++ b/init.el
@@ -56,10 +56,3 @@
   ;; 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-buffer+size-width 40)
- '(Buffer-menu-mode-width 8)
- '(Info-additional-directory-list (quote ("/opt/emacs23/share/info/" 
"/home/gru/info" "/usr/local/share/info")))
- '(Info-auto-generate-directory (quote if-outdated))
- '(Info-button1-follows-hyperlink t)
- '(Info-save-auto-generated-dir (quote always))
- '(LaTeX-command "latex -shell-escape")

[ many lines deleted ]

- '(w3-delay-image-loads t)
- '(w3-do-incremental-display t)
- '(w3-icon-format nil)
- '(w3-maximum-line-length 100)
- '(w3-min-img-size 5)
- '(w3m-use-cookies t)
- '(whitespace-auto-cleanup t)
- '(whitespace-check-spacetab-whitespace nil)
- '(woman-cache-filename "~/.emacs.d/woman-cache.el
-")
- '(woman-imenu t)
- '(woman-use-own-frame nil))
+ '(bmkp-last-as-first-bookmark-file "~/.emacs.bmk"))
 
 
 (custom-set-faces
@@ -266,14 +64,7 @@
   ;; 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 (:stipple nil :background "white" :foreground "black" 
:inverse-video nil :box nil :strike-through nil :overline nil :underline nil 
:slant normal :weight normal :height 80 :width normal :foundry "unknown" 
:family "ProFont"))))
- '(buffer-menu-buffer ((t (:foreground "blue"))))
- '(cursor ((t (:background "blue"))))
- '(highlight ((((class color) (background light)) (:background "gray80"))))
- '(mode-line ((((type x w32 mac) (class color)) (:background "grey75" 
:foreground "black" :box (:line-width -1 :style released-button)))))
- '(org-hide ((((background light)) (:foreground "gray90"))))
- '(show-paren-match ((((class color) (background light)) (:inverse-video t))))
- '(w3m-form ((((class color) (background light)) (:foreground "red" :underline 
t)))))
+ )
 
 ;;============================================================================ 
                                                                                
          ;;{{{ Desktop for saving whole sessions
 ;;++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



any ideas?