Hello everyone, recently I got myself into using emacs and I am really enjoying it. Got myself used to all the basic shortcuts, installed some packages and themes to customize it a bit. Some packages I installed them from within emacs via list-packages from the default package list and from the list of packages by marmalade. Furthermore there are 2 other packages i had to install manually and let them load via the .emacs file on startup. My custom Emacs settings were always persistent even after closing and relaunching emacs several times.

All was going fine I was also doing serious work on it and enjoying it. Then I closed emacs yesterday to shutdown the computer. I launched the editor today and was baffled to see that everything returned to default settings as if it was freshly installed. All the customization in my .emacs and the files in the install-path are all being completely ignored. Even if I try to select a certain(installed) mode such as php-mode it doesnt recognize it anymore.

Any ideas what could be causing this issue?

Here is my .emacs file:

(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.
 '(ansi-color-names-vector ["#2d3743" "#ff4242" "#74af68" "#dbdb95" "#34cae2" "#008b8b" "#00ede1" "#e1e1e0"])
 '(custom-enabled-themes (quote (monokai)))
 '(custom-safe-themes (quote ("b216f5d5060cfececd1f133d71be81b94d2da38c1d099081acf767e931be0506" "71efabb175ea1cf5c9768f10dad62bb2606f41d110152f4ace675325d28df8bd" "c4f5af36d97eebe07ab85faefdc8cd8baa849b1e1b5c7eb6bdd3bff5d4840fec" default))))
(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.
 )
 (add-to-list 'load-path "~/.emacs.d/manual/")

(add-to-list 'auto-mode-alist'())
(global-linum-mode t)

(require 'package)

;; Add the original Emacs Lisp Package Archive
(add-to-list 'package-archives
             '("elpa" . "http://tromey.com/elpa/"))

;; Add the user-contributed repository
(add-to-list 'package-archives
             '("marmalade" . "http://marmalade-repo.org/packages/"))

(setq inhibit-startup-screen t)

(setq backup-directory-alist '(("." . "~/.emacs.d/backup"))
  backup-by-copying t    ; Don't delink hardlinks
  version-control t      ; Use version numbers on backups
  delete-old-versions t  ; Automatically delete excess backups
  kept-new-versions 20   ; how many of the newest versions to keep
  kept-old-versions 5    ; and how many of the old
  )

(require 'web-mode)
(add-to-list 'auto-mode-alist '("\\.phtml\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.tpl\\.php\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.jsp\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.as[cp]x\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.erb\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.mustache\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.djhtml\\'" . web-mode))

Note I am using it on my laptop which runs Windows and not on GNU/Linux.

Furthermore, I never worked with lisp so the lines you see above are merely copy and paste. The syntax highlighting seems messed up here, could it be that there is some syntax error in the file? But if there was, Emacs would alert me on startup that it can't evaluate the file, already came across something like that before and fixed it.